[AMBER] ظAMBER Digest, Vol 1806, Issue 1

From: wei <lwstudy.sina.com>
Date: Sat, 07 Jan 2017 13:42:38 +0800

Thanks a lot for your help, Daniel!
After following your suggestion and modifying my code, now I can obtain exactly the same MSDs magnitudes as Ptraj/Cpptraj's. And I have more confidence for my calculated diffusion coefficient results.
Thanks again.
Best,Liu Wei--------------------------------


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⣺AMBER Digest, Vol 1806, Issue 1
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AMBER Mailing List Digest
Today's Topics:
   1. Re: tLeap and acetonitrile/chloroform solvation (David Case)
   2. Re: compatibility issues (David Case)
   3. Re: compatibility issues (David Case)
   4. Re: tLeap and acetonitrile/chloroform solvation (Luka Bili?)
   5. Re: Problems about membrane protein simulation (??)
   6. Re: tLeap and acetonitrile/chloroform solvation (Luka Bili?)
   7. Re: Problems about membrane protein simulation (Huang Jing)
   8. antechamber: why the net charge does not sum up to zero?
      (Azade Yazdan Yar)
   9. cpptraj clustering doubt (Mary Varughese)
  10. Re: antechamber: why the net charge does not sum up to zero?
      (Hannes Loeffler)
  11. Re: cpptraj clustering doubt (Elvis Martis)
  12. 'Diffusion' calculation in Ptraj - could not understand a
      description of Ptraj code in Amber14 (wei)
  13. Re: cpptraj clustering doubt (Christina Bergonzo)
  14. Re: cpptraj clustering doubt (Daniel Roe)
  15. Re: 'Diffusion' calculation in Ptraj - could not understand a
      description of Ptraj code in Amber14 (Daniel Roe)
  16. Re: Problems about membrane protein simulation (Daniel Roe)
  17. VMD/netcdf (Adrian Roitberg)
  18. Re: cpptraj clustering doubt (Mary Varughese)
  19. cpptraj PCA of crystal structure (anu chandra)
  20. Re: cpptraj PCA of crystal structure (Daniel Roe)
  21. /dev/hfi1_0 device failed to appear after 15 seconds:
      Connection timed out (jacky zhao)
  22. Re: Amber16 on K80 GPUs --poor performance on multiple GPUs
      (Susan Chacko)
  23. Re: compatibility issues (erik rp zuiderweg)
  24. Ion Parameters for tip4pfb (Samaneh Ghassabi Kondalaji)
  25. Re: compatibility issues (Hai Nguyen)
  26. Re: antechamber: why the net charge does not sum up to zero?
      (Jason Swails)
  27. Re: Amber16 on K80 GPUs --poor performance on multiple GPUs
      (Susan Chacko)
----------------------------------------------------------------------
Message: 1
Date: Wed, 4 Jan 2017 21:51:18 -0500
From: David Case <david.case.rutgers.edu>
Subject: Re: [AMBER] tLeap and acetonitrile/chloroform solvation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170105025118.bd5to7mhao2ezi3i.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=utf-8
On Wed, Jan 04, 2017, Luka Bili? wrote:
>
> I am writing to enquire about solvation of organic molecules in Amber 16.
First, you need to make a molecular mechanics description of a single solvent
molecule. This is no different from making files for any organic molecule:
antechamber is probably the most widely-used package, but R.E.D. or a search
engine (I use Google myself, but other search engines exist) are good
alternate approaches.
Once you have files (e.g. mol2 and frcmod) for a *single* solvent molecule,
you need to use that molecule as a solvent.
> How do I use "solvateoct molecule Solvent 14.0" correctly?
> Do I have to have chloroform structure minimized (in Gaussian for
> instance) and then turned into .mol2 file, after which I load it in
> tLeap using "Solvent=loadmol2 Solvent.mol2" or do I have to do
> something else?
What you describe above is the traditional "tleap" approach. This ought to
work, and you don't say what happened when you tried that.
However, I'd strongly recommend an alternate approach: use packmol (not in
Amber) or AddToBox (comes with AmberTools) to create a pdb file with you
solute atom and the desired number of solvent molecules. Then use loadPdb
to load that file into tleap. No need for solvateBox or solvateOct: just
use "set unit box..." to establish the periodic box.
>
> 2nd question/problem
> Since I have found no acetonitrile .lib files. How do I make a solvent
> box containing well defined .frcmod and .lib files. My current .frcmod
> files made from Acetonitrile.mol2 all end up empty.
This is (probably) fine. You don't say exactly what you did, but all the
parameters needed for acetonitrile are already in gaff.dat (or gaff2.dat)
and having an empty frcmod file is OK (you can just delete it.)
....dac
------------------------------
Message: 2
Date: Wed, 4 Jan 2017 21:58:33 -0500
From: David Case <david.case.rutgers.edu>
Subject: Re: [AMBER] compatibility issues
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170105025833.qgzidec5wd5va5dm.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Wed, Jan 04, 2017, Hai Nguyen wrote:
>
> PS1: We've updated info for Mac OS here (much simpler):
> http://ambermd.org/ubuntu.html
The real link is this http://ambermd.org/amber_install.html.
I kept the old file name to preserve git history, but that is probably not
such a good idea.
...dac
------------------------------
Message: 3
Date: Wed, 4 Jan 2017 22:06:03 -0500
From: David Case <david.case.rutgers.edu>
Subject: Re: [AMBER] compatibility issues
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170105030603.ywapva4jdbw4g4rg.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=utf-8
On Wed, Jan 04, 2017, Erik Zuiderweg wrote:
> Mi Amber recompilation failed with errors.
> I now need to reinstall Xcode and the compilers ?.
No getting around this if you upgrade a MacOS to something like Sierra.
But the rest of Amber installation on Macs has been considerably simplified,
as pointed out at http://ambermd.org/amber_install.html. In particular,
there is no need for macports if you don't want it, and don't need it for
other uses. And the back-and-forth here about python 2 vs 3 is only for those
who care...almost all Amber users should just say "yes" when the configure
script offers to download the correct python.
...dac
------------------------------
Message: 4
Date: Thu, 05 Jan 2017 09:09:41 +0100
From: Luka Bili? <Luka.Bilic.irb.hr>
Subject: Re: [AMBER] tLeap and acetonitrile/chloroform solvation
To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170105090941.14756levrj3984sl.webmail.irb.hr>
Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed"
Thank you for your reply!
This was most helpful!
I did try some of these things before (the traditional tLeap approach)
and some worked the way I assumed it will, but now I have confirmation
from you that I was aiming in the right direction.
By using openbabel software I was able to get "real" .mol2 extension
from G09 .log file. Then .frcmod contained some variables. But for now
I will go step by step and learn.
Once more, thank you!
Yours Luka
Citiram David Case <david.case.rutgers.edu>:
> On Wed, Jan 04, 2017, Luka Bili? wrote:
>>
>> I am writing to enquire about solvation of organic molecules in Amber 16.
>
> First, you need to make a molecular mechanics description of a single solvent
> molecule. This is no different from making files for any organic molecule:
> antechamber is probably the most widely-used package, but R.E.D. or a search
> engine (I use Google myself, but other search engines exist) are good
> alternate approaches.
>
> Once you have files (e.g. mol2 and frcmod) for a *single* solvent molecule,
> you need to use that molecule as a solvent.
>
>
>> How do I use "solvateoct molecule Solvent 14.0" correctly?
>> Do I have to have chloroform structure minimized (in Gaussian for
>> instance) and then turned into .mol2 file, after which I load it in
>> tLeap using "Solvent=loadmol2 Solvent.mol2" or do I have to do
>> something else?
>
> What you describe above is the traditional "tleap" approach. This ought to
> work, and you don't say what happened when you tried that.
>
> However, I'd strongly recommend an alternate approach: use packmol (not in
> Amber) or AddToBox (comes with AmberTools) to create a pdb file with you
> solute atom and the desired number of solvent molecules. Then use loadPdb
> to load that file into tleap. No need for solvateBox or solvateOct: just
> use "set unit box..." to establish the periodic box.
>
>>
>> 2nd question/problem
>> Since I have found no acetonitrile .lib files. How do I make a solvent
>> box containing well defined .frcmod and .lib files. My current .frcmod
>> files made from Acetonitrile.mol2 all end up empty.
>
> This is (probably) fine. You don't say exactly what you did, but all the
> parameters needed for acetonitrile are already in gaff.dat (or gaff2.dat)
> and having an empty frcmod file is OK (you can just delete it.)
>
> ....dac
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
------------------------------
Message: 5
Date: Thu, 5 Jan 2017 08:14:51 +0000
From: ?? <wumeng.shanghaitech.edu.cn>
Subject: Re: [AMBER] Problems about membrane protein simulation
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID:
        <E2CAE2DF204D5F4E95C4B8C2959FF0C56668499F.DAGNODE3.shanghaitech.edu.cn>
        
Content-Type: text/plain; charset="gb2312"
Hi,
  I have followed http://archive.ambermd.org/201603/0160.html to use cpptraj to convert the .rst, but the last step 'trajout ###.pdb' kept in 'Writing ### as PDB' state and reported without any errors. Actually, it is my first time to use amber to simulate membrane protein, so besides the above problem, I have two more questions that confused me so much, Q1: In my knowledge, the membrane proteins simulate with the charmm force field commonly, I am not sure whether the amber force field is suitable for membrane proteins or not, and need I add the charmm force field to amber? If I need, how to do it? Q2: Go back to the original problem, I put restraints on protein and POPC molecules at the same time in 'Heat.in',
> restraint_wt=10.0
> restraintmask=':1-486 & !.H=',
is it acceptable to do so? My thought is to restrain the protein and membrane in the whole heating process(NVT), and then release it by decreasing restraints in the early period of the production MD process(NPT), so if this practice is right or not for the membrane protein? Any suggestions would be greatly appreciated. Thank You Very Much!
Sincerely,
Wu Meng
 ###########################################################
Message: 21
Date: Wed, 4 Jan 2017 17:13:16 +0200
From: Huang Jing <jing.huang8911.gmail.com>
Subject: Re: [AMBER] Problems about membrane protein simulation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAMvERa=tBi4OQN8rDWcULrV6qGXvB1OD+Bn8BCb_73y_wLHD7A.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
http://archive.ambermd.org/201603/0160.html
this mail could be useful to solve your problem;
Jing
On Wed, Jan 4, 2017 at 4:44 PM, Shanghaitech University WuMeng <
wumeng.shanghaitech.edu.cn> wrote:
> Dear All,
> I am working on a membrane protein simulation. I have referred to "An
> Amber Lipid Force Field Tutorial:Lipid14 Edition"(http://ambermd.org/
> tutorials/advanced/tutorial16/), the first 'minimization' for my system I
> run is OK, and the next 'Heating' also run successfully, but when I open
> 'Heat.rst' in VMD, nothing displayed in the VMD window, then I tried to use
> ambpdb to transform '.rst' to '.pdb'?there came an error:'Could not read
> restart atoms/time'.(min.rst is OK).It seems there are some mistakes in the
> 'Heat.rst', here is the 'Heat.in':
> ####################
> Heating 100K
> &cntrl
> imin=0,
> ntx=1,
> irest=0,
> ntc=2,
> ntf=2,
> tol=0.0000001,
> nstlim=2500,
> ntt=3,
> gamma_ln=1.0,
> ntr=1,
> ig=-1,
> ntpr=100,
> ntwr=10000,
> ntwx=100,
> dt=0.002,
> nmropt=1,
> ntb=1,
> ntp=0,
> cut=10.0,
> ioutfm=1,
> ntxo=2,
> restraint_wt=10.0
> restraintmask=':1-486 & !.H=',
> /
> &wt
> type='TEMP0',
> istep1=0,
> istep2=2500,
> value1=0.0,
> value2=100.0 /
> &wt type='END' /
> ######################
> I add restraints on protein and POPC molecules(RES 1-486), I don't know
> if it is right or not, this is the first time I use amber to simulate
> membrane protein, so maybe somewhere I missed or did in the wrong way. Any
> suggestions or reference resources about membrane protein simulation would
> be greatly appreciated. Thank You Very Much!
>
>
> Sincerely,
> Wu Meng
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 6
Date: Thu, 05 Jan 2017 09:17:51 +0100
From: Luka Bili? <Luka.Bilic.irb.hr>
Subject: Re: [AMBER] tLeap and acetonitrile/chloroform solvation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170105091751.16973cc8n4ckvodr.webmail.irb.hr>
Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed"
Thank you for your reply.
By using information from your reply (with some trial and error) I was
able to get to the point I desired. Since I'm used to using programs
with complete GUI Amber is quite a joyful challenge.
I realised what was the problem when I was making .frcmod files. It's
not trivial to create .mol2 file from Gaussian09 .log file. Openbabel
software provided me with a proper .mol2 file. In other words I
converted Gaussian09 .log file into .mol2 using Openbabel and this in
return gave me complete .mol2 file from which I was able to make
non-empty .frcmod file.
For now this is not so important, Gaff2 has everything I currently
need. However later when (if?) I will be doing some things in unusual
solvents I might need to play with some solvent parameters.
Anyway, thank you for pointing me in the right direction!
I hope I will be able to return to favor one day.
Yours Luka
Citiram Huang Jing <jing.huang8911.gmail.com>:
> Here is a tutorial to have a typical molecular dynamics; you could follow
> the procedures in this tuturial and then it would be easy to manage your
> own molecules;
> http://ambermd.org/tutorials/basic/tutorial0/
>
> 1st question:
> Following is the command in the manual;
>> mol = loadpdb my.pdb
>> solvateOct mol TIP3PBOX 12.0 0.75
>
> 2nd question:
> Use "antechamber" to creat the .mol2 and .frcmod for the non-library
> molecules;
> http://ambermd.org/tutorials/basic/tutorial4b/
>
> jing
>
>
> On Wed, Jan 4, 2017 at 4:12 PM, Luka Bili? <Luka.Bilic.irb.hr> wrote:
>
>> To whom it may concern,
>>
>> I am writing to enquire about solvation of organic molecules in Amber 16.
>> So far I've had some troubles in navigating tutorials and manual in
>> regards to solvating a molecule in acetonitrile or chloroform. So this
>> e-mail will contain 2 questions/problems with similar content.
>>
>> 1st question/problem:
>> I've found that the Amber 16 has "solvents.lib" and appropriate frcmod
>> file for chloroform, but I am not sure how to use this to solvate my
>> molecule of interest with this. My molecule of interest is a .log file
>> from Gaussian optimisation. I have used antechamber to change it in
>> .mol2 file type so I can work with it in Amber 16. Now I will present
>> an input feed so you may see where Currently I'm unable to continue
>> without help or advice but I will try to understand this on my own in
>> the meantime.
>>
>> "
>> tleap
>> -I: Adding /home/user/amber16/dat/leap/prep to search path. -I: Adding
>> /home/user/amber16/dat/leap/lib to search path.
>> -I: Adding /home/user/amber16/dat/leap/parm to search path.
>> -I: Adding /home/user/amber16/dat/leap/cmd to search path.
>>
>> Welcome to LEaP!
>> (no leaprc in search path)
>> source leaprc.gaff2
>> ----- Source: /home/user/amber16/dat/leap/cmd/leaprc.gaff2 -----
>> Source of /home/user/amber16/dat/leap/cmd/leaprc.gaff2 done
>> Log file: ./leap.log
>> Loading parameters: /home/user/amber16/dat/leap/parm/gaff2.dat
>> Reading title:
>> AMBER General Force Field for organic molecules (Version 2.1, April 2016)
>> loadamberparams frcmod.chcl3
>> Loading parameters: /home/user/amber16/dat/leap/parm/frcmod.chcl3
>> Reading force field modification type file (frcmod)
>> Reading title:
>> chloroform frcmod file
>> "
>>
>> So the next obvious step would be to define what my molecule of
>> interest is by adding line
>>
>> "molecule=loadmol2 MoleculeOfInterest.mol2"
>>
>> And from this spot troubles arise.
>>
>> How do I use "solvateoct molecule Solvent 14.0" correctly?
>> Do I have to have chloroform structure minimized (in Gaussian for
>> instance) and then turned into .mol2 file, after which I load it in
>> tLeap using "Solvent=loadmol2 Solvent.mol2" or do I have to do
>> something else?
>>
>> 2nd question/problem
>> Since I have found no acetonitrile .lib files. How do I make a solvent
>> box containing well defined .frcmod and .lib files. My current .frcmod
>> files made from Acetonitrile.mol2 all end up empty.
>>
>> .frcmod
>> "
>> remark goes here
>> MASS
>>
>> BOND
>>
>> ANGLE
>>
>> DIHE
>>
>> IMPROPER
>>
>> NONBON
>> "
>> In other words, (how) can I make my own explicit acetonitrile
>> parameters for solvation of organic molecules in order to do MD
>> simulations. This question may be generalized to: How do I make custom
>> solvent parameters and how do I use them for explicit solvation of
>> molecules (organic molecules, metal complex compounds and proteins).
>>
>> If this all seems trivial to someone, please understand that this is
>> the 5th day of my life where I'm trying to do something in Amber. I do
>> not want to go blindly through tutorials because that will give me
>> false sense of knowledge and skills (both of which will take months,
>> if not years to properly acquire).
>>
>> Also thank you for your understanding and help.
>>
>> Yours Luka
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
------------------------------
Message: 7
Date: Thu, 5 Jan 2017 11:31:40 +0200
From: Huang Jing <jing.huang8911.gmail.com>
Subject: Re: [AMBER] Problems about membrane protein simulation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAMvERakie2EN3LNW1kcxqnujfqiHMh8LdbGCLQQnRPPmvBQkkQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
It is very strange to have so much special character for the
"restraintmask" keyword;
the definition of restraintmask would be,
> restraintmask=':1-486',
Jing
On Thu, Jan 5, 2017 at 10:14 AM, ?? <wumeng.shanghaitech.edu.cn> wrote:
> Hi,
> I have followed http://archive.ambermd.org/201603/0160.html to use
> cpptraj to convert the .rst, but the last step 'trajout ###.pdb' kept in
> 'Writing ### as PDB' state and reported without any errors. Actually, it is
> my first time to use amber to simulate membrane protein, so besides the
> above problem, I have two more questions that confused me so much, Q1: In
> my knowledge, the membrane proteins simulate with the charmm force field
> commonly, I am not sure whether the amber force field is suitable for
> membrane proteins or not, and need I add the charmm force field to amber?
> If I need, how to do it? Q2: Go back to the original problem, I put
> restraints on protein and POPC molecules at the same time in 'Heat.in',
>
> > restraint_wt=10.0
> > restraintmask=':1-486 & !.H=',
>
> is it acceptable to do so? My thought is to restrain the protein and
> membrane in the whole heating process(NVT), and then release it by
> decreasing restraints in the early period of the production MD
> process(NPT), so if this practice is right or not for the membrane protein?
> Any suggestions would be greatly appreciated. Thank You Very Much!
>
> Sincerely,
> Wu Meng
>
> ###########################################################
> Message: 21
> Date: Wed, 4 Jan 2017 17:13:16 +0200
> From: Huang Jing <jing.huang8911.gmail.com>
> Subject: Re: [AMBER] Problems about membrane protein simulation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAMvERa=tBi4OQN8rDWcULrV6qGXvB1OD+Bn8BCb_73y_wLHD7A.mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> http://archive.ambermd.org/201603/0160.html
> this mail could be useful to solve your problem;
>
> Jing
>
> On Wed, Jan 4, 2017 at 4:44 PM, Shanghaitech University WuMeng <
> wumeng.shanghaitech.edu.cn> wrote:
>
> > Dear All,
> > I am working on a membrane protein simulation. I have referred to "An
> > Amber Lipid Force Field Tutorial:Lipid14 Edition"(http://ambermd.org/
> > tutorials/advanced/tutorial16/), the first 'minimization' for my system
> I
> > run is OK, and the next 'Heating' also run successfully, but when I open
> > 'Heat.rst' in VMD, nothing displayed in the VMD window, then I tried to
> use
> > ambpdb to transform '.rst' to '.pdb'?there came an error:'Could not read
> > restart atoms/time'.(min.rst is OK).It seems there are some mistakes in
> the
> > 'Heat.rst', here is the 'Heat.in':
> > ####################
> > Heating 100K
> > &cntrl
> > imin=0,
> > ntx=1,
> > irest=0,
> > ntc=2,
> > ntf=2,
> > tol=0.0000001,
> > nstlim=2500,
> > ntt=3,
> > gamma_ln=1.0,
> > ntr=1,
> > ig=-1,
> > ntpr=100,
> > ntwr=10000,
> > ntwx=100,
> > dt=0.002,
> > nmropt=1,
> > ntb=1,
> > ntp=0,
> > cut=10.0,
> > ioutfm=1,
> > ntxo=2,
> > restraint_wt=10.0
> > restraintmask=':1-486 & !.H=',
> > /
> > &wt
> > type='TEMP0',
> > istep1=0,
> > istep2=2500,
> > value1=0.0,
> > value2=100.0 /
> > &wt type='END' /
> > ######################
> > I add restraints on protein and POPC molecules(RES 1-486), I don't know
> > if it is right or not, this is the first time I use amber to simulate
> > membrane protein, so maybe somewhere I missed or did in the wrong way.
> Any
> > suggestions or reference resources about membrane protein simulation
> would
> > be greatly appreciated. Thank You Very Much!
> >
> >
> > Sincerely,
> > Wu Meng
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 8
Date: Thu, 5 Jan 2017 11:52:34 +0100
From: Azade Yazdan Yar <azade.yazdanyar.gmail.com>
Subject: [AMBER] antechamber: why the net charge does not sum up to
        zero?
To: amber.ambermd.org
Message-ID:
        <CAGJydFR753ULme9aYAp-5PgdVmi5Qb0E7my+nFBBF91U3bZjnw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hello everyone,
I have a problem similar to here <http://archive.ambermd.org/all/2855.html>.
Unfortunately, I did not find an answer to that inquiry.
I am using antechamber on a pdb file to create the mol2 file.
The molecule should be charge neutral and I am using ?-c bcc ?nc 0? flags.
However, the sum of the charges in the output.mol2 generated by antechamber
is not 0.0.
I also tried ?-ek maxcyc=0? flag on several initial.pdb files (point 7,
P.277 of the manual) which all of them lead to a non-zero net charge. The
smallest net charge which I can get is 0.001.
My question is whether or not this net charge is small enough so I can work
with it or is there is another trick which I can use?
Thanks a lot for your help.
Sincerely,
Azade
------------------------------
Message: 9
Date: Thu, 5 Jan 2017 16:29:52 +0530
From: Mary Varughese <maryvj1985.gmail.com>
Subject: [AMBER] cpptraj clustering doubt
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAAjRZU1k7Kg+WvPpdA4H54ti5NU=N9+r4+p4wL97d0h272a1rQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Sir
in combined clustering, could i compare more than two trajectories? If
so is there any difference in the command option
split ..Frameno...
Also in split_summary.dat is there any useful information.
how could i infer the convergence of the trajectory DBI , pSF
Please give me some idea
Thanking you
mary varughese
------------------------------
Message: 10
Date: Thu, 5 Jan 2017 11:06:06 +0000
From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Subject: Re: [AMBER] antechamber: why the net charge does not sum up
        to zero?
To: <amber.ambermd.org>
Message-ID: <20170105110606.74389669.stfc.ac.uk>
Content-Type: text/plain; charset="UTF-8"
On Thu, 5 Jan 2017 11:52:34 +0100
Azade Yazdan Yar <azade.yazdanyar.gmail.com> wrote:
> The molecule should be charge neutral and I am using ?-c bcc ?nc 0?
> flags. However, the sum of the charges in the output.mol2 generated
> by antechamber is not 0.0.
>
> [...]
>
> My question is whether or not this net charge is small enough so I
> can work with it or is there is another trick which I can use?
This question comes up here from time to time e.g. I have answered this
once here
http://archive.ambermd.org/all/80369.html
------------------------------
Message: 11
Date: Thu, 5 Jan 2017 11:41:22 +0000
From: "Elvis Martis" <elvis.martis.bcp.edu.in>
Subject: Re: [AMBER] cpptraj clustering doubt
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <BM1PR01MB011518D595B25FC42D2E437BA3600.BM1PR01MB0115.INDPRD01.PROD.OUTLOOK.COM>
        
Content-Type: text/plain; charset="iso-8859-1"
Yes, this is possible. Please follow this link http://www.amber.utah.edu/AMBER-workshop/London-2015/Cluster/
And also read the paper by Shao et al http://pubs.acs.org/doi/abs/10.1021/ct700119m?journalCode=jctcce .
They have explained all you need to know.
? ? Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
?at?Bombay College of Pharmacy
A??Kalina, Santacruz [E], Mumbai 400098, INDIA
W?www.elvismartis.in
Skype.?adrian_elvis12
-----Original Message-----
From: Mary Varughese [mailto:maryvj1985.gmail.com]
Sent: Thursday, January 05, 2017 4:30 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] cpptraj clustering doubt
Sir
in combined clustering, could i compare more than two trajectories? If so is there any difference in the command option split ..Frameno...
Also in split_summary.dat is there any useful information.
how could i infer the convergence of the trajectory DBI , pSF
Please give me some idea
Thanking you
mary varughese
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 12
Date: Thu, 05 Jan 2017 20:39:40 +0800
From: "wei" <lwstudy.sina.com>
Subject: [AMBER] 'Diffusion' calculation in Ptraj - could not
        understand a description of Ptraj code in Amber14
To: "amber" <amber.ambermd.org>
Message-ID: <20170105123940.3309E4013B.webmail.sinamail.sina.com.cn>
Content-Type: text/plain; charset=GBK
Dear all,
I want to verify that the translational diffusion constant I calculated for a sugar molecule is correct. I found that the magnitudes of mean square displacement (MSD) for one atom I computed using Ptraj/Cpptraj is fairly different from what I obtained from a small code I wrote (I just read in coordinates for all atoms directly then calculate MSDs as follows:
open(11,file='image.crd')do read(11,*) read(11,'(10f8.3)') (x(i),y(i),z(i),i=1,natom) nframe=nframe+1 cx(nframe)=x(1) cy(nframe)=y(1) cz(nframe)=z(1)enddoclose(11)
do t=0,2000 do i=1,nframe-t dvx(t+1)=dvx(t+1)+(cx(i+t)-cx(i))**2 dvy(t+1)=dvy(t+1)+(cy(i+t)-cy(i))**2 dvz(t+1)=dvz(t+1)+(cz(i+t)-cz(i))**2 enddo dvx(t+1)=dvx(t+1)/real(nframe-t) dvy(t+1)=dvy(t+1)/real(nframe-t) dvz(t+1)=dvz(t+1)/real(nframe-t)enddo).
Ptraj input was wrote as:
diffusion :1.C1 2 average output
Then I got (MSD for a specific t):Mine code (239.17)Ptraj (936.91)
Thus I am reading the code related to 'diffusion' command in Ptraj (please find it in AMBER14, 'actions.c'). I feel confused while seeing these lines of comments:
/* * if the particle moved more than half the box, assume * it was imaged and adjust the distance of the total * movement with respect to the original frame... */ if ( state->box[0] > 0.0 ) { if ( delx > state->box[0]/2.0 ) diffusionInfo->deltax[currentAtom] -= state->box[0]; else if ( delx < -state->box[0]/2.0 ) diffusionInfo->deltax[currentAtom] += state->box[0]; if ( dely > state->box[1]/2.0 ) diffusionInfo->deltay[currentAtom] -= state->box[1]; else if ( dely < -state->box[1]/2.0 ) diffusionInfo->deltay[currentAtom] += state->box[1]; if ( delz > state->box[2]/2.0 ) diffusionInfo->deltaz[currentAtom] -= state->box[2]; else if ( delz < -state->box[2]/2.0 ) diffusionInfo->deltaz[currentAtom] += state->box[2]; }
I am just trying to find the reason why I did not compute the same MSDs as Ptraj. I have two simple question:1. How to understand this description--"adjust the distance of the total movement with respect to the original frame"? Does 'total movement' refer to external degrees of freedom of the simulated box?2. Ptraj images atoms for all frames or just for those frames whose particle moved more than half the box?
Any help would be highly appreciated and thanks in advance!
Regards,Liu Wei--------------------------------
------------------------------
Message: 13
Date: Thu, 5 Jan 2017 07:48:21 -0500
From: Christina Bergonzo <cbergonzo.gmail.com>
Subject: Re: [AMBER] cpptraj clustering doubt
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAMLwDJ08nOjrBgxGuOoXC9m=chxoe-isT6gK=ib2=+X5ryTa4g.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
You can take a look at the supporting information of this paper:
Highly sampled tetranucleotide and tetraloop motifs enable evaluation of
common RNA force fields
<https://scholar.google.com/citations?view_op=view_citation&hl=en&user=d4JoelsAAAAJ&citation_for_view=d4JoelsAAAAJ:In6cVmBjs0IC>
C Bergonzo, NM Henriksen, DR Roe, TE Cheatham
RNA 21 (9), 1578-1590
http://rnajournal.cshlp.org/content/suppl/2015/06/19/rna.051102.115.DC1/SuppMaterial.pdf
There is a CPPTRAJ command which performs combined clustering on 8
trajectories.
Hope this helps,
Christina
On Thu, Jan 5, 2017 at 5:59 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
> Sir
>
>
> in combined clustering, could i compare more than two trajectories? If
> so is there any difference in the command option
> split ..Frameno...
>
> Also in split_summary.dat is there any useful information.
>
> how could i infer the convergence of the trajectory DBI , pSF
>
> Please give me some idea
>
>
> Thanking you
>
>
> mary varughese
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-- 
---------------------------------------------------------------------------------------
Christina Bergonzo
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
http://home.chpc.utah.edu/~cheatham/
---------------------------------------------------------------------------------------
------------------------------
Message: 14
Date: Thu, 5 Jan 2017 08:30:50 -0500
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] cpptraj clustering doubt
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAAC0qOZVuw5H+5TF5_n3eP7VjmbySAns9Qd3Zz6ui6R0YoVwDg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
See also the clustering script in part 7 of the supporting info here:
http://pubs.acs.org/doi/abs/10.1021/jp4125099
-Dan
On Thu, Jan 5, 2017 at 7:48 AM, Christina Bergonzo <cbergonzo.gmail.com> wrote:
> Hi,
>
> You can take a look at the supporting information of this paper:
> Highly sampled tetranucleotide and tetraloop motifs enable evaluation of
> common RNA force fields
> <https://scholar.google.com/citations?view_op=view_citation&hl=en&user=d4JoelsAAAAJ&citation_for_view=d4JoelsAAAAJ:In6cVmBjs0IC>
> C Bergonzo, NM Henriksen, DR Roe, TE Cheatham
> RNA 21 (9), 1578-1590
>
> http://rnajournal.cshlp.org/content/suppl/2015/06/19/rna.051102.115.DC1/SuppMaterial.pdf
>
> There is a CPPTRAJ command which performs combined clustering on 8
> trajectories.
>
> Hope this helps,
> Christina
>
> On Thu, Jan 5, 2017 at 5:59 AM, Mary Varughese <maryvj1985.gmail.com> wrote:
>
>> Sir
>>
>>
>> in combined clustering, could i compare more than two trajectories? If
>> so is there any difference in the command option
>> split ..Frameno...
>>
>> Also in split_summary.dat is there any useful information.
>>
>> how could i infer the convergence of the trajectory DBI , pSF
>>
>> Please give me some idea
>>
>>
>> Thanking you
>>
>>
>> mary varughese
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ---------------------------------------------------------------------------------------
> Christina Bergonzo
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> http://home.chpc.utah.edu/~cheatham/
> ---------------------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
------------------------------
Message: 15
Date: Thu, 5 Jan 2017 08:52:17 -0500
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] 'Diffusion' calculation in Ptraj - could not
	understand a description of Ptraj code in Amber14
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAAC0qOY9H=1AkCJ1oV3GmfViZGJWXsgU-GL1YcvoY3+9j6q-oA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
For some reason your message came in all in a single line (i.e. there
were no newlines) which made reading your code a little difficult, but
I've spotted some problems:
On Thu, Jan 5, 2017 at 7:39 AM, wei <lwstudy.sina.com> wrote:
> Dear all,
> I want to verify that the translational diffusion constant I calculated for a sugar molecule is correct. I found that the magnitudes of mean square displacement (MSD) for one atom I computed using Ptraj/Cpptraj is fairly different from what I obtained from a small code I wrote (I just read in coordinates for all atoms directly then calculate MSDs as follows:
> open(11,file='image.crd')
> do
>  read(11,*)
>  read(11,'(10f8.3)') (x(i),y(i),z(i),i=1,natom)
>  nframe=nframe+1
>  cx(nframe)=x(1)
>  cy(nframe)=y(1)
>  cz(nframe)=z(1)
> enddo
> close(11)
This code is incorrect for reading Amber ASCII trajectories. The title
line only appears once (see
http://ambermd.org/formats.html#trajectory). You need to move the
'read(11,*)' statement to outside the do loop. Also, if your
trajectory has any box coordinates they need to be read after the
coordinates. A good check to see if your code is doing the right thing
is to try and write the data back out and see if you can visualize it.
> do t=0,2000
>  do i=1,nframe-t
>    dvx(t+1)=dvx(t+1)+(cx(i+t)-cx(i))**2
>    dvy(t+1)=dvy(t+1)+(cy(i+t)-cy(i))**2
>    dvz(t+1)=dvz(t+1)+(cz(i+t)-cz(i))**2
>  enddo
>  dvx(t+1)=dvx(t+1)/real(nframe-t)
>  dvy(t+1)=dvy(t+1)/real(nframe-t)
>  dvz(t+1)=dvz(t+1)/real(nframe-t)
>enddo).
This isn't the right calculation for mean-squared displacement. You
want the average of the delta of each from from the *initial* frame
because you want to know how far a particle moved (i.e. was displaced)
from it's initial position, not how far it is moving each frame on
average (see also
https://en.wikipedia.org/wiki/Mean_squared_displacement). It looks
like you're doing some kind of correlation calculation above.
> Ptraj input was wrote as:
> diffusion :1.C1 2 average output
> Then I got (MSD for a specific t):Mine code (239.17)Ptraj          (936.91)
> Thus I am reading the code related to 'diffusion' command in Ptraj (please find it in AMBER14, 'actions.c'). I feel confused while seeing these lines of comments:
> /*       *  if the particle moved more than half the box, assume       *  it was imaged and adjust the distance of the total       *  movement with respect to the original frame...       */      if ( state->box[0] > 0.0 ) {        if ( delx > state->box[0]/2.0 )          diffusionInfo->deltax[currentAtom] -= state->box[0];        else if ( delx < -state->box[0]/2.0 )          diffusionInfo->deltax[currentAtom] += state->box[0];        if ( dely > state->box[1]/2.0 )          diffusionInfo->deltay[currentAtom] -= state->box[1];        else if ( dely < -state->box[1]/2.0 )          diffusionInfo->deltay[currentAtom] += state->box[1];        if ( delz > state->box[2]/2.0 )          diffusionInfo->deltaz[currentAtom] -= state->box[2];        else if ( delz < -state->box[2]/2.0 )          diffusionInfo->deltaz[currentAtom] += state->box[2];      }
This is the code in ptraj that attempts to account for imaging in
orthorhombic cells. As I wrote previously, if you don't 'unwrap' an
imaged trajectory prior to the diffusion calculation, you have to
correct for imaging "jumps", otherwise you get the wrong value for
diffusion. Cpptraj does this for both orthorhombic and
non-orthorhombic cells.
Hope this helps,
-Dan
> I am just trying to find the reason why I did not compute the same MSDs as Ptraj. I have two simple question:1. How to understand this description--"adjust the distance of the total movement with respect to the original frame"? Does 'total movement' refer to external degrees of freedom of the simulated box?2. Ptraj images atoms for all frames or just for those frames whose particle moved more than half the box?
> Any help would be highly appreciated and thanks in advance!
> Regards,Liu Wei--------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
------------------------------
Message: 16
Date: Thu, 5 Jan 2017 09:14:14 -0500
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Problems about membrane protein simulation
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAAC0qOYS2qCqA_BD_HdicNruxes6Qei9NDxuUROWbM=ODScKAQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
On Thu, Jan 5, 2017 at 3:14 AM, ?? <wumeng.shanghaitech.edu.cn> wrote:
> Hi,
>   I have followed http://archive.ambermd.org/201603/0160.html to use cpptraj to convert the .rst, but the last step 'trajout ###.pdb' kept in 'Writing ### as PDB' state and reported without any errors.
Do you mean cpptraj was hanging and not writing the PDB? Did it exit
with an error? Were you running interactively and didn't actually type
'run'. Could you provide some more details? Does something like
'cpptraj -p <topology file> -y heat.rst -x heat.pdb' not work? I
suspect your original issue is that the default restart format for
Amber16 is NetCDF which VMD does not yet read (although I think
support is coming soon).
> Actually, it is my first time to use amber to simulate membrane protein, so besides the above problem, I have two more questions that confused me so much, Q1: In my knowledge, the membrane proteins simulate with the charmm force field commonly, I am not sure whether the amber force field is suitable for membrane proteins or not, and need I add the charmm force field to amber?
See section '3.4 Lipids' in the Amber 16 manual and references
therein, particularly http://pubs.acs.org/doi/abs/10.1021/ct4010307.
> If I need, how to do it?  Q2: Go back to the original problem, I put restraints on protein and POPC molecules at the same time in 'Heat.in',
>
>>   restraint_wt=10.0
>>   restraintmask=':1-486 & !.H=',
>
> is it acceptable to do so? My thought is to restrain the protein and membrane in the whole heating process(NVT), and then release it by decreasing restraints in the early period of the production MD process(NPT), so if this practice is right or not for the membrane protein? Any suggestions would be greatly appreciated. Thank You Very Much!
That restraintmask looks fine, but 10.0 seems like quite a high force
constant. I would start at no more than 5. Also, you probably want to
gradually reduce the restraint weight in successive runs until you can
eliminate it.
-Dan
>
> Sincerely,
> Wu Meng
>
>  ###########################################################
> Message: 21
> Date: Wed, 4 Jan 2017 17:13:16 +0200
> From: Huang Jing <jing.huang8911.gmail.com>
> Subject: Re: [AMBER] Problems about membrane protein simulation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
>         <CAMvERa=tBi4OQN8rDWcULrV6qGXvB1OD+Bn8BCb_73y_wLHD7A.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> http://archive.ambermd.org/201603/0160.html
> this mail could be useful to solve your problem;
>
> Jing
>
> On Wed, Jan 4, 2017 at 4:44 PM, Shanghaitech University WuMeng <
> wumeng.shanghaitech.edu.cn> wrote:
>
>> Dear All,
>>   I am working on a membrane  protein simulation. I have referred to "An
>> Amber Lipid Force Field Tutorial:Lipid14 Edition"(http://ambermd.org/
>> tutorials/advanced/tutorial16/), the first 'minimization' for my system I
>> run is OK, and the next 'Heating' also run successfully, but when I open
>> 'Heat.rst' in VMD, nothing displayed in the VMD window, then I tried to use
>> ambpdb to transform '.rst' to '.pdb'?there came an error:'Could not read
>> restart atoms/time'.(min.rst is OK).It seems there are some mistakes in the
>> 'Heat.rst', here is the 'Heat.in':
>> ####################
>> Heating 100K
>>  &cntrl
>>   imin=0,
>>   ntx=1,
>>   irest=0,
>>   ntc=2,
>>   ntf=2,
>>   tol=0.0000001,
>>   nstlim=2500,
>>   ntt=3,
>>   gamma_ln=1.0,
>>   ntr=1,
>>   ig=-1,
>>   ntpr=100,
>>   ntwr=10000,
>>   ntwx=100,
>>   dt=0.002,
>>   nmropt=1,
>>   ntb=1,
>>   ntp=0,
>>   cut=10.0,
>>   ioutfm=1,
>>   ntxo=2,
>>   restraint_wt=10.0
>>   restraintmask=':1-486 & !.H=',
>>  /
>>  &wt
>>   type='TEMP0',
>>   istep1=0,
>>   istep2=2500,
>>   value1=0.0,
>>   value2=100.0 /
>>  &wt type='END' /
>> ######################
>> I add restraints on protein and POPC molecules(RES 1-486), I don't  know
>> if it is right or not, this is the first time I use amber to simulate
>> membrane protein, so maybe somewhere I missed or did in the wrong way. Any
>> suggestions or reference resources about membrane protein simulation would
>> be greatly  appreciated. Thank You Very Much!
>>
>>
>> Sincerely,
>> Wu Meng
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
------------------------------
Message: 17
Date: Thu, 5 Jan 2017 10:09:50 -0500
From: Adrian Roitberg <roitberg.ufl.edu>
Subject: [AMBER] VMD/netcdf
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <e6533899-1338-a1c1-c863-d79de9595f75.ufl.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear All
Thanks to John Stone (VMD head developer), vmd can now read the default 
binary netcdf format for amber16 restart files.
Just load the prmtop as usual and then load the restart file as netcdf 
in the file format menu.
You need vmd 1.9.3 to do this, and as always, windows does not know how 
to read netcdf files.
adrian
-- 
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
------------------------------
Message: 18
Date: Thu, 5 Jan 2017 20:53:38 +0530
From: Mary Varughese <maryvj1985.gmail.com>
Subject: Re: [AMBER] cpptraj clustering doubt
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAAjRZU09FzzD+biP8YS5DwBp3LBhup2CnqvUxi_ntWyTMEnn+Q.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Thank you very much.
It was very much helpful especially that script in supp material.
Thank you
On Thu, Jan 5, 2017 at 7:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> See also the clustering script in part 7 of the supporting info here:
> http://pubs.acs.org/doi/abs/10.1021/jp4125099
>
> -Dan
>
> On Thu, Jan 5, 2017 at 7:48 AM, Christina Bergonzo <cbergonzo.gmail.com>
> wrote:
> > Hi,
> >
> > You can take a look at the supporting information of this paper:
> > Highly sampled tetranucleotide and tetraloop motifs enable evaluation of
> > common RNA force fields
> > <https://scholar.google.com/citations?view_op=view_citation&hl=en&user=
> d4JoelsAAAAJ&citation_for_view=d4JoelsAAAAJ:In6cVmBjs0IC>
> > C Bergonzo, NM Henriksen, DR Roe, TE Cheatham
> > RNA 21 (9), 1578-1590
> >
> > http://rnajournal.cshlp.org/content/suppl/2015/06/19/rna.
> 051102.115.DC1/SuppMaterial.pdf
> >
> > There is a CPPTRAJ command which performs combined clustering on 8
> > trajectories.
> >
> > Hope this helps,
> > Christina
> >
> > On Thu, Jan 5, 2017 at 5:59 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> >
> >> Sir
> >>
> >>
> >> in combined clustering, could i compare more than two trajectories? If
> >> so is there any difference in the command option
> >> split ..Frameno...
> >>
> >> Also in split_summary.dat is there any useful information.
> >>
> >> how could i infer the convergence of the trajectory DBI , pSF
> >>
> >> Please give me some idea
> >>
> >>
> >> Thanking you
> >>
> >>
> >> mary varughese
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > ------------------------------------------------------------
> ---------------------------
> > Christina Bergonzo
> > Postdoctoral Researcher
> > Department of Medicinal Chemistry, University of Utah
> > http://home.chpc.utah.edu/~cheatham/
> > ------------------------------------------------------------
> ---------------------------
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 19
Date: Thu, 5 Jan 2017 16:25:48 +0000
From: anu chandra <anu80125.gmail.com>
Subject: [AMBER] cpptraj PCA of crystal structure
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CADEHHN=_kDwwQ1CznH9Zx5jL_u5Q1zX7eWG97UtzsDZ=1Cbqcw.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hello all,
I am trying to project the crystal structure of a protein with 210
aminoacids, into top two PC (principle component) space. For this, I have
carried out PCA of crystal structure with the following script.
Unfortunately, all modes came out as zeros. The crystal structure was
obtained from PDB. Am I doing anything wrong here?.
------------------------------------------------------------------------------------------------------
parm 1atm.pdb
trajin 1atm.pdb
createcrd crd1
run
crdaction crd1 matrix covar !.H= name gaccCovar
runanalysis diagmatrix gaccCovar vecs 2 name evecs
crdaction crd1 projection T1 modes evecs beg 1 end 2 !.H= out T1.dat
-----------------------------------------------------------------------------------------------------------
Any help would be highly appreciated
Many thanks
Anu
------------------------------
Message: 20
Date: Thu, 5 Jan 2017 11:30:14 -0500
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] cpptraj PCA of crystal structure
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAAC0qOZ8BOxLzXXthu2iFh+usbyre3v9GWoCJUPDqyhKB51q6Q.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
It makes no sense to do principal component analysis on a single
trajectory frame (there is no motion to analyze!). The coordinate
covariance matrix should be constructed from at least as many frames
as you have coordinates, otherwise you will have eigenvectors with
zero eigenvalues. Maybe you wanted to do normal mode analysis? In that
case you should use the 'nab' program. See the Amber16 manual for
details.
-Dan
On Thu, Jan 5, 2017 at 11:25 AM, anu chandra <anu80125.gmail.com> wrote:
> Hello all,
>
> I am trying to project the crystal structure of a protein with 210
> aminoacids, into top two PC (principle component) space. For this, I have
> carried out PCA of crystal structure with the following script.
> Unfortunately, all modes came out as zeros. The crystal structure was
> obtained from PDB. Am I doing anything wrong here?.
>
> ------------------------------------------------------------------------------------------------------
> parm 1atm.pdb
>
>
> trajin 1atm.pdb
>
> createcrd crd1
> run
>
> crdaction crd1 matrix covar !.H= name gaccCovar
>
> runanalysis diagmatrix gaccCovar vecs 2 name evecs
>
> crdaction crd1 projection T1 modes evecs beg 1 end 2 !.H= out T1.dat
> -----------------------------------------------------------------------------------------------------------
>
>
> Any help would be highly appreciated
>
>
> Many thanks
> Anu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
-- 
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
------------------------------
Message: 21
Date: Fri, 6 Jan 2017 00:34:46 +0800
From: jacky zhao <jackyzhao010.gmail.com>
Subject: [AMBER] /dev/hfi1_0 device failed to appear after 15 seconds:
	Connection timed out
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CA+LvrWPMaUC41abbkmh+SqULEHbn0R4L49FXmLjaeVcCy7jCeQ.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi everyone
 I have compiled Amber16 on my  workstation, which have passed amber test
without any failed. But when I run Amber16_benchmark_suite, the following
information appear: DESKTOP-NODMRU7.lan.1720hfi_wait_for_device: The
/dev/hfi1_0 device failed to appear after 15 seconds: Connection timed out.
Have you anyone give me some suggestions to solve this problem?
Thank you for taking your time.
Jacky
------------------------------
Message: 22
Date: Thu, 5 Jan 2017 11:41:00 -0500
From: Susan Chacko <susanc.helix.nih.gov>
Subject: Re: [AMBER] Amber16 on K80 GPUs --poor performance on
	multiple GPUs
To: amber.ambermd.org
Message-ID: <1074c1a5-d700-6710-1980-4febca064e8f.helix.nih.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
I had read that and tried adding the --bind-to-none flag, but it didn't 
make a difference. I've also tried explicitly allocating CPUs with 
'taskset', selecting CPUs that are on the same socket as the GPUs.
There are no other jobs running on this K80 node: just my one benchmark 
run.
I have a little additional information to add now. We have both K20xs 
and K80s in our cluster. For the Factor IX NPT benchmark:
K20x, 1 GPU:  31.94 ns/day
K20x, 2 GPU: 30.97 ns/day
K80, 1 GPU:   30.26 ns/day
K80, 2 GPU:   1.13 ns/day
Thus, the K20x's behave similar to my benchmarks with Amber14. I only 
see the big drop in performance with the K80s.
The instruction sets for the K20xs are different from the K80s.
K20x: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat 
pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb 
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology 
nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est 
tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt 
tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb 
xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep 
erms
K80: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat 
pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb 
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology 
nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est 
tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt 
tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb 
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase 
bmi1 avx2 smep bmi2 erms invpcid cqm cqm_llc cqm_occup_llc
I had originally built on the K20x, so that the executable would run on 
either type of GPU. I tried rebuilding on the K80, but even with this 
K80-built executable, I'm still getting ~30 ns/day on 1 K80, and ~1 
ns/day on 2 K80s.
One thing I noticed is that I see 4 processes running on 2 K80 GPUs, 
while only 2 processes run on 2 K20 GPUs. i.e.
K20x nvidia-smi:
+------------------------------------------------------+
| NVIDIA-SMI 352.39     Driver Version: 352.39         |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile 
Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util 
Compute M. |
|===============================+======================+======================|
|   0  Tesla K20Xm         On   | 0000:08:00.0     Off 
|                  Off |
| N/A   33C    P0    97W / 235W |    275MiB /  6143MiB | 62%      Default |
+-------------------------------+----------------------+----------------------+
|   1  Tesla K20Xm         On   | 0000:27:00.0     Off 
|                  Off |
| N/A   35C    P0   103W / 235W |    333MiB /  6143MiB | 71%      Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
|  GPU       PID  Type  Process name Usage      |
|=============================================================================|
|    0     55048    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI   
259MiB |
|    1     55049    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI   
317MiB |
+-----------------------------------------------------------------------------+
K80x nvidia-smi:
+------------------------------------------------------+
| NVIDIA-SMI 352.39     Driver Version: 352.39         |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile 
Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util 
Compute M. |
|===============================+======================+======================|
|   0  Tesla K80           Off  | 0000:83:00.0     Off 
|                    0 |
| N/A   34C    P8    27W / 149W |     22MiB / 11519MiB | 0%      Default |
+-------------------------------+----------------------+----------------------+
|   1  Tesla K80           Off  | 0000:84:00.0     Off 
|                    0 |
| N/A   26C    P8    31W / 149W |     22MiB / 11519MiB | 0%      Default |
+-------------------------------+----------------------+----------------------+
|   2  Tesla K80           Off  | 0000:8A:00.0     Off 
|                    0 |
| N/A   75C    P0    73W / 149W |    349MiB / 11519MiB | 99%      Default |
+-------------------------------+----------------------+----------------------+
|   3  Tesla K80           Off  | 0000:8B:00.0     Off 
|                    0 |
| N/A   49C    P0    80W / 149W |    407MiB / 11519MiB | 99%      Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
|  GPU       PID  Type  Process name Usage      |
|=============================================================================|
|    2     29646    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI   
258MiB |
|    2     29647    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI    
64MiB |
|    3     29646    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI    
64MiB |
|    3     29647    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI   
316MiB |
+-----------------------------------------------------------------------------+
Is this significant? I'm running the exact same command and executable 
on both types of GPUs, i.e.
mpirun  --bind-to none -np 2 `which pmemd.cuda.MPI` -O -i mdin.GPU -o 
mdout -p prmtop -c inpcrd
The CPU processes look fine, i.e. both the K20x and K80s show 2 MPI CPU 
processes.
Susan
On 1/4/17 8:05 AM, Ross Walker wrote:
> Hi Susan,
>
> Please see the following:
>
> http://ambermd.org/gpus/#Max_Perf <http://ambermd.org/gpus/#Max_Perf>
>
> particularly item 10 with regards to OpenMPI. I reproduced it here for convenience but I'd recommend reading the whole page.
>
>
> 10. If you see that performance when running multiple - multi-GPU runs is bad. That is that say you run 2 x 2GPU jobs and they don't both run at full speed as if the other job was never running then make sure you turn off thread affinity within your MPI implementation or at least set each MPI thread to use a difference core. In my experience MPICH does not have this on by default and so no special settings are needed however both MVAPICH and OpenMPI  set thread affinity by default. This would actually be useful if they did it in an intelligent way. However, it seems they pay no attention to load or even other MVAPICH or OpenMPI runs and always just assign from core 0. So 2 x 2 GPU jobs are, rather foolishly, assigned to cores 0 and 1 in both cases. The simplest solution here is to just disable thread affinity as follows:
>
> MVAPICH: export MV2_ENABLE_AFFINITY=0; mpirun -np 2 ...
> OpenMPI: mpirun --bind-to none -np 2 ...
>
> All the best
> Ross
>
>
>> On Jan 3, 2017, at 12:36, Susan Chacko <susanc.helix.nih.gov> wrote:
>>
>>   According to mdout, peer-to-peer support is enabled.
>>
>> |------------------- GPU DEVICE INFO --------------------
>> |
>> |                         Task ID:      0
>> |            CUDA_VISIBLE_DEVICES: not set
>> |   CUDA Capable Devices Detected:      4
>> |           CUDA Device ID in use:      0
>> |                CUDA Device Name: Tesla K80
>> |     CUDA Device Global Mem Size:  11519 MB
>> | CUDA Device Num Multiprocessors:     13
>> |           CUDA Device Core Freq:   0.82 GHz
>> |
>> |
>> |                         Task ID:      1
>> |            CUDA_VISIBLE_DEVICES: not set
>> |   CUDA Capable Devices Detected:      4
>> |           CUDA Device ID in use:      1
>> |                CUDA Device Name: Tesla K80
>> |     CUDA Device Global Mem Size:  11519 MB
>> | CUDA Device Num Multiprocessors:     13
>> |           CUDA Device Core Freq:   0.82 GHz
>> |
>> |--------------------------------------------------------
>>
>> |---------------- GPU PEER TO PEER INFO -----------------
>> |
>> |   Peer to Peer support: ENABLED
>>
>>
>> I also downloaded and ran the check_p2p program from the Amber site, and
>> got:
>>
>> -----------
>>
>> % ./gpuP2PCheck
>> CUDA_VISIBLE_DEVICES is unset.
>> CUDA-capable device count: 4
>>     GPU0 "      Tesla K80"
>>     GPU1 "      Tesla K80"
>>     GPU2 "      Tesla K80"
>>     GPU3 "      Tesla K80"
>>
>> Two way peer access between:
>>     GPU0 and GPU1: YES
>>     GPU0 and GPU2: YES
>>     GPU0 and GPU3: YES
>>     GPU1 and GPU2: YES
>>     GPU1 and GPU3: YES
>>     GPU2 and GPU3: YES
>>
>> -----------
>>
>> So in theory I should be able to run on up to 4 GPUs.
>> I'll try rebuilding with CUDA 8.0 next, as Huang Jing suggested, unless
>> anyone else has other ideas.
>>
>> Susan.
>>
>>
>> On 1/3/17 11:25 AM, Daniel Roe wrote:
>>> Hi,
>>>
>>> See the 'Multi GPU' section in http://ambermd.org/gpus/#Running for
>>> some tips. In particular you need to make sure that the GPUs can run
>>> with direct peer-to-peer communication to get any kind of speedup for
>>> multi GPUs (this is printed somewhere near the top of mdout output).
>>>
>>> -Dan
>>>
>>> On Tue, Jan 3, 2017 at 11:00 AM, Susan Chacko <susanc.helix.nih.gov> wrote:
>>>> Hi all,
>>>>
>>>> I successfully built Amber 16 with Intel 2015.1.133, CUDA 7.5, and
>>>> OpenMPI 2.0.1. We're running Centos 6.8 and Nvidia drivers 352.39 on
>>>> K80x GPUs.
>>>>
>>>> I ran the benchmark suite. I'm getting approx the same results as shown
>>>> on the Amber16 benchmark page for CPUs and 1 GPU
>>>> (http://ambermd.org/gpus/benchmarks.htm)
>>>>
>>>> e.g.
>>>>
>>>> Factor IX NPT
>>>>
>>>> Intel E5-2695 v3 . 2.30GHz, 28 cores: 9.58 ns/day
>>>>
>>>> 1 K80 GPU: 31.2 ns/day
>>>>
>>>> However, when I attempt to run on 2 K80 GPUs, performance drops
>>>> dramatically.
>>>> 2 K80 GPUs: 1.19 ns/day
>>>>
>>>> I'm running the pmemd.cuda_SPFP.MPI executable like this:
>>>> cd Amber16_Benchmark_Suite/PME/FactorIX_production_NPT
>>>> mpirun -np # /usr/local/apps/amber/amber16/bin/pmemd.cuda_SPFP.MPI -O -i
>>>> mdin.GPU -o mdout -p prmtop -c inpcrd
>>>> where # is 1 or 2.
>>>> Each of the individual GPUs ran this benchmark at ~31.2 ns/day, so I
>>>> don't think there is any intrinsic problem with any of GPU hardware.
>>>> I get the same drop in performance with pmemd.cuda_DPFP.MPI and
>>>> pmemd.cuda_SPXP.MPI
>>>>
>>>> Is this expected behaviour? I don't see a benchmark for 2 or more K80s
>>>> on the Amber16 GPUs benchmark page, so am not sure what to expect. I
>>>> also see that the benchmarks on that page were run with Amber16/ Centos
>>>> 7 + CUDA 8.0 + MPICH 3.1.4 and are running on later versions of the
>>>> Nvidia drivers than we have, but I would not expect those differences to
>>>> account for what I'm seeing.
>>>>
>>>> Any ideas? Is it worth rebuilding with CUDA 8.0, or MPICH instead of
>>>> OpenMPI?
>>>>
>>>> All thoughts and suggestions much appreciated,
>>>> Susan.
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> -- 
>> Susan Chacko, Ph.D.
>> HPC . NIH Staff
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
-- 
Susan Chacko, Ph.D.
HPC . NIH Staff
------------------------------
Message: 23
Date: Thu, 5 Jan 2017 18:33:53 +0100
From: erik rp zuiderweg <zuiderwe.umich.edu>
Subject: Re: [AMBER] compatibility issues
To: david.case.rutgers.edu, AMBER Mailing List <amber.ambermd.org>
Message-ID: <4378E42D-E7E0-40FC-A3F5-D3D02E73C7C0.umich.edu>
Content-Type: text/plain; charset=utf-8
Making progress ?
having my GNU compilers (vs.6.1.0) reinstalled with XCode8.1 on MacOS 10.11.6 and running.
Now trying to reinstall AMBER11
Starting in amber11/Ambertools/src 
I changed  the configure file to point to the new compilers.
then successfully issued the commands
./configure -macAccelerate gnu    ?> OK
make clean   ?> OK
make 
runs fine, and complies a gazillion things, also fortran codes,  but then chokes on
gfortran-6.1.0 -c -O0 -ffree-form  -o qm2_pm6_hof_module.o _qm2_pm6_hof_module.f
_qm2_pm6_hof_module.f:109:41:
   double precision function hofCorrection()
                                         1
Error: In generic interface 'pm6_correction' at (1) procedures must be either all SUBROUTINEs or all FUNCTIONs 
Seems to be a compiler incompatibility.
Can you help? Or should I just buy Amber16 (OK with me too)
Erik Zuiderweg
University of Michigan
zuiderwe.umich.edu
(734) 276 4463
> On Jan 5, 2017, at 4:06 AM, David Case <david.case.rutgers.edu> wrote:
> 
> On Wed, Jan 04, 2017, Erik Zuiderweg wrote:
> 
>> Mi Amber recompilation failed with errors.
>> I now need to reinstall Xcode and the compilers ?.
> 
> No getting around this if you upgrade a MacOS to something like Sierra.
> 
> But the rest of Amber installation on Macs has been considerably simplified,
> as pointed out at http://ambermd.org/amber_install.html.  In particular,
> there is no need for macports if you don't want it, and don't need it for
> other uses.  And the back-and-forth here about python 2 vs 3 is only for those
> who care...almost all Amber users should just say "yes" when the configure
> script offers to download the correct python.
> 
> ...dac
> 
> 
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 24
Date: Thu, 5 Jan 2017 12:44:25 -0500
From: Samaneh Ghassabi Kondalaji <saghassabikondalaji.mix.wvu.edu>
Subject: [AMBER] Ion Parameters for tip4pfb
To: amber.ambermd.org
Message-ID:
	<CAGx1a2x3e-Ta4_jZRw+uHjDoU5jHreiS+rE9M5DfuKB8iw=qKA.mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
?Dear Amber developers and users
    I am attempting to use tip4pfb water model to solvate a peptide.
Initially I sourced the leaprc.protein.ff14SB file in addition to loading
solvents.lib, frcmod.tip4pfb and atomic_ions.lib files. After solvating the
peptide in FB4BOX, using the addions (or addions2) I added 2 Na+ ions
without any errors (the Na+ exists in Unit list). However, when I try to
save the prmtop and inpcrd files, I get this error (leap.log file is
attached to this E-mail):
*For atom: .R<Na+ 520>.A<Na+ 1> Could not find vdW (or other) parameters
for type: Na+*
    Now, I understand that I need to source ion parameters using files such
as leaprc.water.tip4pewFB4 and frcmod.ionsjc_tip4pewFB4 for FB4BOX water
model, except that these files do not exist. Any suggestions on how I can
find these parameters would be greatly appreciated.
Best Regards
samaneh
?P.S. The system is a peptide (ACE LYS NME) with overall charge state of +3
in water. The error message does not appear when I use tip3fb water model
with related force field files.
-- 
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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------------------------------
Message: 25
Date: Thu, 5 Jan 2017 12:45:05 -0500
From: Hai Nguyen <nhai.qn.gmail.com>
Subject: Re: [AMBER] compatibility issues
To: AMBER Mailing List <amber.ambermd.org>
Cc: David A Case <david.case.rutgers.edu>
Message-ID:
	<CAFNMPM89m7nSWmDzXbUt0wh7GesAW3-GVhSs4eCM7xAANHqXOA.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Please upgrade to AmberTools16 (free anyway).
Using clang:
./configure -macAccelerate clang
Using GNU
./configure gnu
Hai
On Thu, Jan 5, 2017 at 12:33 PM, erik rp zuiderweg <zuiderwe.umich.edu>
wrote:
> Making progress ?
> having my GNU compilers (vs.6.1.0) reinstalled with XCode8.1 on MacOS
> 10.11.6 and running.
>
> Now trying to reinstall AMBER11
>
> Starting in amber11/Ambertools/src
> I changed  the configure file to point to the new compilers.
> then successfully issued the commands
> ./configure -macAccelerate gnu    ?> OK
> make clean   ?> OK
>
> make
> runs fine, and complies a gazillion things, also fortran codes,  but then
> chokes on
>
> gfortran-6.1.0 -c -O0 -ffree-form  -o qm2_pm6_hof_module.o
> _qm2_pm6_hof_module.f
> _qm2_pm6_hof_module.f:109:41:
>
>    double precision function hofCorrection()
>                                          1
> Error: In generic interface 'pm6_correction' at (1) procedures must be
> either all SUBROUTINEs or all FUNCTIONs
>
> Seems to be a compiler incompatibility.
>
> Can you help? Or should I just buy Amber16 (OK with me too)
>
>
>
>
>
> Erik Zuiderweg
> University of Michigan
> zuiderwe.umich.edu
> (734) 276 4463
>
> > On Jan 5, 2017, at 4:06 AM, David Case <david.case.rutgers.edu> wrote:
> >
> > On Wed, Jan 04, 2017, Erik Zuiderweg wrote:
> >
> >> Mi Amber recompilation failed with errors.
> >> I now need to reinstall Xcode and the compilers ?.
> >
> > No getting around this if you upgrade a MacOS to something like Sierra.
> >
> > But the rest of Amber installation on Macs has been considerably
> simplified,
> > as pointed out at http://ambermd.org/amber_install.html.  In particular,
> > there is no need for macports if you don't want it, and don't need it for
> > other uses.  And the back-and-forth here about python 2 vs 3 is only for
> those
> > who care...almost all Amber users should just say "yes" when the
> configure
> > script offers to download the correct python.
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 26
Date: Thu, 5 Jan 2017 12:55:23 -0500
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] antechamber: why the net charge does not sum up
	to zero?
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
	<CAEk9e3pwfEV9TJ4-CeZD87uzJqvHV=MihLm6_4B2kD6AJUypMg.mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Thu, Jan 5, 2017 at 5:52 AM, Azade Yazdan Yar <azade.yazdanyar.gmail.com>
wrote:
> Hello everyone,
>
>
>
> I have a problem similar to here <http://archive.ambermd.org/
> all/2855.html>.
> Unfortunately, I did not find an answer to that inquiry.
>
> I am using antechamber on a pdb file to create the mol2 file.
>
> The molecule should be charge neutral and I am using ?-c bcc ?nc 0? flags.
> However, the sum of the charges in the output.mol2 generated by antechamber
> is not 0.0.
>
> I also tried ?-ek maxcyc=0? flag on several initial.pdb files (point 7,
> P.277 of the manual) which all of them lead to a non-zero net charge. The
> smallest net charge which I can get is 0.001.
>
> My question is whether or not this net charge is small enough so I can work
> with it or is there is another trick which I can use?
>
?The only comment I'll make in addition to what Hannes said is that unless
you plan on using the generated mol2 file as a template for a solvent
molecule -- that is, unless you plan on including many thousands of copies
of this residue in your system -- the round-off error of 0.01 to 0.001 will
make little to no difference (values this small get smeared over every atom
in the system by sander and pmemd).
If you plan on including many thousands of copies, then the net charge may
start to become significant (although the net neutralizing plasma will
still be able to handle this excess charge for most applications).
However, ParmEd has the ability to redistribute this excess charge to yield
a set of charges that round to an exact integer for any level of precision
you want in the charges.
This can be accomplished with a quick Python script that looks like this:
import parmed as pmd
pmd.load_file('your_file.mol2').fix_charges(precision=4).save('fixed_charges.mol2')
This needs to be invoked with the amber.python interpreter to make sure
that ParmEd can be found.  However, as mentioned before, unless you plan on
including thousands of copies of this residue in your system, there is
nothing to worry about.
HTH,
Jason
-- 
Jason M. Swails
------------------------------
Message: 27
Date: Thu, 5 Jan 2017 14:15:30 -0500
From: Susan Chacko <susanc.helix.nih.gov>
Subject: Re: [AMBER] Amber16 on K80 GPUs --poor performance on
	multiple GPUs
To: amber.ambermd.org
Message-ID: <9b7fd63c-8cf8-87fb-852a-59ae2fb8aff6.helix.nih.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
Ah, someone suggested backchannel that I should try setting the 
CUDA_VISIBLE_DEVICES to ensure that 2 GPUs were being used.
deviceQuery says there are 2 devices called 0 and 1
% ./deviceQuery -noprompt | egrep "^Device"
Device 0: "Tesla K80"
Device 1: "Tesla K80"
but nvidia-smi says there are 4.
+------------------------------------------------------+
| NVIDIA-SMI 352.39     Driver Version: 352.39         |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile 
Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util 
Compute M. |
|===============================+======================+======================|
|   0  Tesla K80           Off  | 0000:83:00.0     Off 
|                    0 |
| N/A   45C    P0    57W / 149W |     22MiB / 11519MiB | 0%      Default |
+-------------------------------+----------------------+----------------------+
|   1  Tesla K80           Off  | 0000:84:00.0     Off 
|                    0 |
| N/A   31C    P0    72W / 149W |     22MiB / 11519MiB | 0%      Default |
+-------------------------------+----------------------+----------------------+
|   2  Tesla K80           Off  | 0000:8A:00.0     Off 
|                    0 |
| N/A   47C    P0    59W / 149W |     22MiB / 11519MiB | 0%      Default |
+-------------------------------+----------------------+----------------------+
|   3  Tesla K80           Off  | 0000:8B:00.0     Off 
|                    0 |
| N/A   36C    P0    71W / 149W |     22MiB / 11519MiB | 94%      Default |
+-------------------------------+----------------------+----------------------+
I tried all combinations of the 4 GPU devices in pairs:
CUDA_VISIBLE_DEVICES=0,1   nvidia-smi reports devices 2,3 are being 
used.     Performance:     ~1 ns/day
CUDA_VISIBLE_DEVICES=0,2   nvidia-smi reports devices 0,2 are being 
used.     Performance:    ~44 ns/day
CUDA_VISIBLE_DEVICES=0,3    nvidia-smi reports devices 1,2 are being 
used.    Performance:  ~44 ns/day
CUDA_VISIBLE_DEVICES=1,2    nvidia-smi reports devices 0,3 are being 
used.    Performance:  ~44 ns/day
CUDA_VISIBLE_DEVICES=1,3    nvidia-smi reports devices 1,3 are being 
used.    Performance:  ~44 ns/day
CUDA_VISIBLE_DEVICES=2,3   nvidia-smi reports devices  0,1 are being 
used.    Performance:  ~1 ns/day
Confusing! Anyway, now that I am able to run the benchmark and get 44 
ns/day performance, i know there's nothing intrinsically wrong with the 
build. I'll do some more research into our GPUs and how the GPU devices 
are labelled.
Many thanks to everyone who offered suggestions, either here or backchannel,
Susan.
On 1/5/17 11:41 AM, Susan Chacko wrote:
> I had read that and tried adding the --bind-to-none flag, but it didn't
> make a difference. I've also tried explicitly allocating CPUs with
> 'taskset', selecting CPUs that are on the same socket as the GPUs.
>
> There are no other jobs running on this K80 node: just my one benchmark
> run.
>
> I have a little additional information to add now. We have both K20xs
> and K80s in our cluster. For the Factor IX NPT benchmark:
>
> K20x, 1 GPU:  31.94 ns/day
> K20x, 2 GPU: 30.97 ns/day
>
> K80, 1 GPU:   30.26 ns/day
> K80, 2 GPU:   1.13 ns/day
>
> Thus, the K20x's behave similar to my benchmarks with Amber14. I only
> see the big drop in performance with the K80s.
>
> The instruction sets for the K20xs are different from the K80s.
> K20x: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat
> pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb
> rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology
> nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est
> tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt
> tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm ida arat epb
> xsaveopt pln pts dts tpr_shadow vnmi flexpriority ept vpid fsgsbase smep
> erms
>
> K80: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat
> pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb
> rdtscp lm constant_tsc arch_perfmon pebs bts rep_good xtopology
> nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est
> tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt
> tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb
> xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase
> bmi1 avx2 smep bmi2 erms invpcid cqm cqm_llc cqm_occup_llc
>
> I had originally built on the K20x, so that the executable would run on
> either type of GPU. I tried rebuilding on the K80, but even with this
> K80-built executable, I'm still getting ~30 ns/day on 1 K80, and ~1
> ns/day on 2 K80s.
>
> One thing I noticed is that I see 4 processes running on 2 K80 GPUs,
> while only 2 processes run on 2 K20 GPUs. i.e.
>
> K20x nvidia-smi:
> +------------------------------------------------------+
> | NVIDIA-SMI 352.39     Driver Version: 352.39         |
> |-------------------------------+----------------------+----------------------+
> | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile
> Uncorr. ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util
> Compute M. |
> |===============================+======================+======================|
> |   0  Tesla K20Xm         On   | 0000:08:00.0     Off
> |                  Off |
> | N/A   33C    P0    97W / 235W |    275MiB /  6143MiB | 62%      Default |
> +-------------------------------+----------------------+----------------------+
> |   1  Tesla K20Xm         On   | 0000:27:00.0     Off
> |                  Off |
> | N/A   35C    P0   103W / 235W |    333MiB /  6143MiB | 71%      Default |
> +-------------------------------+----------------------+----------------------+
>
> +-----------------------------------------------------------------------------+
> | Processes: GPU Memory |
> |  GPU       PID  Type  Process name Usage      |
> |=============================================================================|
> |    0     55048    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI
> 259MiB |
> |    1     55049    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI
> 317MiB |
> +-----------------------------------------------------------------------------+
>
> K80x nvidia-smi:
> +------------------------------------------------------+
> | NVIDIA-SMI 352.39     Driver Version: 352.39         |
> |-------------------------------+----------------------+----------------------+
> | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile
> Uncorr. ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util
> Compute M. |
> |===============================+======================+======================|
> |   0  Tesla K80           Off  | 0000:83:00.0     Off
> |                    0 |
> | N/A   34C    P8    27W / 149W |     22MiB / 11519MiB | 0%      Default |
> +-------------------------------+----------------------+----------------------+
> |   1  Tesla K80           Off  | 0000:84:00.0     Off
> |                    0 |
> | N/A   26C    P8    31W / 149W |     22MiB / 11519MiB | 0%      Default |
> +-------------------------------+----------------------+----------------------+
> |   2  Tesla K80           Off  | 0000:8A:00.0     Off
> |                    0 |
> | N/A   75C    P0    73W / 149W |    349MiB / 11519MiB | 99%      Default |
> +-------------------------------+----------------------+----------------------+
> |   3  Tesla K80           Off  | 0000:8B:00.0     Off
> |                    0 |
> | N/A   49C    P0    80W / 149W |    407MiB / 11519MiB | 99%      Default |
> +-------------------------------+----------------------+----------------------+
>
> +-----------------------------------------------------------------------------+
> | Processes: GPU Memory |
> |  GPU       PID  Type  Process name Usage      |
> |=============================================================================|
> |    2     29646    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI
> 258MiB |
> |    2     29647    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI
> 64MiB |
> |    3     29646    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI
> 64MiB |
> |    3     29647    C ...cal/apps/amber/amber16/bin/pmemd.cuda.MPI
> 316MiB |
> +-----------------------------------------------------------------------------+
>
> Is this significant? I'm running the exact same command and executable
> on both types of GPUs, i.e.
>
> mpirun  --bind-to none -np 2 `which pmemd.cuda.MPI` -O -i mdin.GPU -o
> mdout -p prmtop -c inpcrd
>
> The CPU processes look fine, i.e. both the K20x and K80s show 2 MPI CPU
> processes.
>
> Susan
>
> On 1/4/17 8:05 AM, Ross Walker wrote:
>> Hi Susan,
>>
>> Please see the following:
>>
>> http://ambermd.org/gpus/#Max_Perf <http://ambermd.org/gpus/#Max_Perf>
>>
>> particularly item 10 with regards to OpenMPI. I reproduced it here for convenience but I'd recommend reading the whole page.
>>
>>
>> 10. If you see that performance when running multiple - multi-GPU runs is bad. That is that say you run 2 x 2GPU jobs and they don't both run at full speed as if the other job was never running then make sure you turn off thread affinity within your MPI implementation or at least set each MPI thread to use a difference core. In my experience MPICH does not have this on by default and so no special settings are needed however both MVAPICH and OpenMPI  set thread affinity by default. This would actually be useful if they did it in an intelligent way. However, it seems they pay no attention to load or even other MVAPICH or OpenMPI runs and always just assign from core 0. So 2 x 2 GPU jobs are, rather foolishly, assigned to cores 0 and 1 in both cases. The simplest solution here is to just disable thread affinity as follows:
>>
>> MVAPICH: export MV2_ENABLE_AFFINITY=0; mpirun -np 2 ...
>> OpenMPI: mpirun --bind-to none -np 2 ...
>>
>> All the best
>> Ross
>>
>>
>>> On Jan 3, 2017, at 12:36, Susan Chacko <susanc.helix.nih.gov> wrote:
>>>
>>>    According to mdout, peer-to-peer support is enabled.
>>>
>>> |------------------- GPU DEVICE INFO --------------------
>>> |
>>> |                         Task ID:      0
>>> |            CUDA_VISIBLE_DEVICES: not set
>>> |   CUDA Capable Devices Detected:      4
>>> |           CUDA Device ID in use:      0
>>> |                CUDA Device Name: Tesla K80
>>> |     CUDA Device Global Mem Size:  11519 MB
>>> | CUDA Device Num Multiprocessors:     13
>>> |           CUDA Device Core Freq:   0.82 GHz
>>> |
>>> |
>>> |                         Task ID:      1
>>> |            CUDA_VISIBLE_DEVICES: not set
>>> |   CUDA Capable Devices Detected:      4
>>> |           CUDA Device ID in use:      1
>>> |                CUDA Device Name: Tesla K80
>>> |     CUDA Device Global Mem Size:  11519 MB
>>> | CUDA Device Num Multiprocessors:     13
>>> |           CUDA Device Core Freq:   0.82 GHz
>>> |
>>> |--------------------------------------------------------
>>>
>>> |---------------- GPU PEER TO PEER INFO -----------------
>>> |
>>> |   Peer to Peer support: ENABLED
>>>
>>>
>>> I also downloaded and ran the check_p2p program from the Amber site, and
>>> got:
>>>
>>> -----------
>>>
>>> % ./gpuP2PCheck
>>> CUDA_VISIBLE_DEVICES is unset.
>>> CUDA-capable device count: 4
>>>      GPU0 "      Tesla K80"
>>>      GPU1 "      Tesla K80"
>>>      GPU2 "      Tesla K80"
>>>      GPU3 "      Tesla K80"
>>>
>>> Two way peer access between:
>>>      GPU0 and GPU1: YES
>>>      GPU0 and GPU2: YES
>>>      GPU0 and GPU3: YES
>>>      GPU1 and GPU2: YES
>>>      GPU1 and GPU3: YES
>>>      GPU2 and GPU3: YES
>>>
>>> -----------
>>>
>>> So in theory I should be able to run on up to 4 GPUs.
>>> I'll try rebuilding with CUDA 8.0 next, as Huang Jing suggested, unless
>>> anyone else has other ideas.
>>>
>>> Susan.
>>>
>>>
>>> On 1/3/17 11:25 AM, Daniel Roe wrote:
>>>> Hi,
>>>>
>>>> See the 'Multi GPU' section in http://ambermd.org/gpus/#Running for
>>>> some tips. In particular you need to make sure that the GPUs can run
>>>> with direct peer-to-peer communication to get any kind of speedup for
>>>> multi GPUs (this is printed somewhere near the top of mdout output).
>>>>
>>>> -Dan
>>>>
>>>> On Tue, Jan 3, 2017 at 11:00 AM, Susan Chacko <susanc.helix.nih.gov> wrote:
>>>>> Hi all,
>>>>>
>>>>> I successfully built Amber 16 with Intel 2015.1.133, CUDA 7.5, and
>>>>> OpenMPI 2.0.1. We're running Centos 6.8 and Nvidia drivers 352.39 on
>>>>> K80x GPUs.
>>>>>
>>>>> I ran the benchmark suite. I'm getting approx the same results as shown
>>>>> on the Amber16 benchmark page for CPUs and 1 GPU
>>>>> (http://ambermd.org/gpus/benchmarks.htm)
>>>>>
>>>>> e.g.
>>>>>
>>>>> Factor IX NPT
>>>>>
>>>>> Intel E5-2695 v3 . 2.30GHz, 28 cores: 9.58 ns/day
>>>>>
>>>>> 1 K80 GPU: 31.2 ns/day
>>>>>
>>>>> However, when I attempt to run on 2 K80 GPUs, performance drops
>>>>> dramatically.
>>>>> 2 K80 GPUs: 1.19 ns/day
>>>>>
>>>>> I'm running the pmemd.cuda_SPFP.MPI executable like this:
>>>>> cd Amber16_Benchmark_Suite/PME/FactorIX_production_NPT
>>>>> mpirun -np # /usr/local/apps/amber/amber16/bin/pmemd.cuda_SPFP.MPI -O -i
>>>>> mdin.GPU -o mdout -p prmtop -c inpcrd
>>>>> where # is 1 or 2.
>>>>> Each of the individual GPUs ran this benchmark at ~31.2 ns/day, so I
>>>>> don't think there is any intrinsic problem with any of GPU hardware.
>>>>> I get the same drop in performance with pmemd.cuda_DPFP.MPI and
>>>>> pmemd.cuda_SPXP.MPI
>>>>>
>>>>> Is this expected behaviour? I don't see a benchmark for 2 or more K80s
>>>>> on the Amber16 GPUs benchmark page, so am not sure what to expect. I
>>>>> also see that the benchmarks on that page were run with Amber16/ Centos
>>>>> 7 + CUDA 8.0 + MPICH 3.1.4 and are running on later versions of the
>>>>> Nvidia drivers than we have, but I would not expect those differences to
>>>>> account for what I'm seeing.
>>>>>
>>>>> Any ideas? Is it worth rebuilding with CUDA 8.0, or MPICH instead of
>>>>> OpenMPI?
>>>>>
>>>>> All thoughts and suggestions much appreciated,
>>>>> Susan.
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> -- 
>>> Susan Chacko, Ph.D.
>>> HPC . NIH Staff
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
-- 
Susan Chacko, Ph.D.
HPC . NIH Staff
------------------------------
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Received on Fri Jan 06 2017 - 22:00:02 PST
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