Hello David,
Thank you for the quick response.
1. My AmberTools17 is fully updated (./configure returns with no patches available for AmberTools 17).
2. I have CUDA 9.0
3. When enter “which gcc” I receive the output “usr/bin/gcc” as you predicted.
4. “./configure -clang ?” may have been a typo. I am using the command “./configure -cuda clang” to which I get the error:
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 17 patches:
No patches available
Available Amber 16 patches:
No patches available
AMBER_PREFIX=/Users/kadirozcan/amber16
AMBER_SOURCE=/Users/kadirozcan/amber16
Using the AmberTools miniconda installation in /Users/kadirozcan/amber16/miniconda
version 2.7.13
CUDA Version 9.0 detected
Configuring for SM3.0, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1 and SM7.0
Obtaining the clang compiler suite versions, e.g.:
clang -v
Error: clang is not well formed or produces unusual version details!
Check for a CC environment variable.
Configure failed due to the errors above!
Thank you once again.
On Apr 17, 2018, at 3:00 PM, amber-request.ambermd.org<mailto:amber-request.ambermd.org> wrote:
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AMBER Mailing List Digest
Today's Topics:
1. Re: Cpptraj and Sander Question (Portillo, Jennifer)
2. Configure cuda (Kadir Ozcan)
3. convert psf to prmtop (Ashutosh Shandilya)
4. Re: Configure cuda (David A Case)
5. Re: convert psf to prmtop (David A Case)
6. Re: Regarding AuCl force field (David A Case)
7. Re: md simulation of modified nucleotides in RNA (FyD)
8. Re: convert psf to prmtop (Jason Swails)
9. Re: Replica exchange in explicit solvent (Maya Hauss)
10. Weight the xyz components of restraints (Huan He)
11. Re: Simple normal mode analysis in amber (Lorena.Rosaleny.uv.es<mailto:Lorena.Rosaleny.uv.es>)
12. Re: Replica exchange in explicit solvent
(Cruzeiro,Vinicius Wilian D)
13. Re: Simple normal mode analysis in amber (David A Case)
14. QMMM Replica exchange with TeraChem (Raimon Fabregat)
15. How fast is Amber's new GPU code? Are CPUs ever coming back?
(David Cerutti)
----------------------------------------------------------------------
Message: 1
Date: Mon, 16 Apr 2018 14:10:42 -0700
From: "Portillo, Jennifer" <
jennifer.portillo.387.my.csun.edu<mailto:
jennifer.portillo.387.my.csun.edu>>
Subject: Re: [AMBER] Cpptraj and Sander Question
To: david.case.rutgers.edu<mailto:david.case.rutgers.edu>, AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Message-ID:
<
CAP3ZqEXJcR1Vkx91-ACy1ESRE_V1c+xUPYf+w3ekKM-EX7-Suw.mail.gmail.com<mailto:
CAP3ZqEXJcR1Vkx91-ACy1ESRE_V1c+xUPYf+w3ekKM-EX7-Suw.mail.gmail.com>>
Content-Type: text/plain; charset="UTF-8"
Thanks for the email. We are using AmberTools17.
The line 244 of $AMBERHOME/AmberTools/src/sander/rdparm.F90
is reading iscratch and ffdesc. I don?t know what that section is for.
Here is the code:
230 ! format should be (nlines, text) where we read the first lines
nlines
231 ! to know how many more lines to read - we ignore nlines on
subsequent
232 ! lines but they still need to be there.
233 ! e.g.
234 ! 2 PARM99
235 ! 2 GAFF
236 read(nf,fmt) nlines,line
237 allocate (ffdesc(nlines), stat = ierr)
238 REQUIRE(ierr==0)
239 ffdesc(1) = line
240 #ifndef API
241 write(6,'(a,a)') '| ',ffdesc(1)
242 #endif
243 do i = 2, nlines
244 read(nf,fmt) iscratch,ffdesc(i)
245 #ifndef API
246 write(6,'(a,a)') '| ',ffdesc(i)
247 #endif
248 end do
On Wed, Apr 11, 2018 at 5:15 AM, David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>>
wrote:
On Tue, Apr 10, 2018, Portillo, Jennifer wrote:
At line 244 of file rdparm.F90 (unit = 8, file = 'protein.prmtop')
Can you look at line 244 of $AMBERHOME/AmberTools/src/sander/rdparm.F90,
and see what section of the prmtop file is being read? (I don't know
what version of AmberTools you have, so cannot be sure where to look
myself.)
Once you know which section of the prmtop file is being read, you can
look to see if there is something odd about your file in that section.
...good luck....dac
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------------------------------
Message: 2
Date: Mon, 16 Apr 2018 23:53:15 +0000
From: Kadir Ozcan <Kadir.Ozcan.jefferson.edu<mailto:Kadir.Ozcan.jefferson.edu>>
Subject: [AMBER] Configure cuda
To: "amber.ambermd.org<mailto:amber.ambermd.org>" <amber.ambermd.org<mailto:amber.ambermd.org>>
Message-ID: <4AB11483-EF5B-45A3-BF10-6C4C8387FBCC.jefferson.edu<mailto:4AB11483-EF5B-45A3-BF10-6C4C8387FBCC.jefferson.edu>>
Content-Type: text/plain; charset="utf-8"
Hello all,
I am attempting to configure cuda on a MacOS High Sierra Version 10.13.1 with an external GeForce GTX 980 Ti. When I enter the code listed in the manual:
export CUDA_HOME=/Developer/NVIDIA/CUDA-9.0
cd $AMBERHOME
./configure -cuda gnu
I get the following error message from ? ./configure -cuda gnu ?:
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 17 patches:
No patches available
Available Amber 16 patches:
No patches available
AMBER_PREFIX=/Users/kadirozcan/amber16
AMBER_SOURCE=/Users/kadirozcan/amber16
Using the AmberTools miniconda installation in /Users/kadirozcan/amber16/miniconda
version 2.7.13
CUDA Version 9.0 detected
Configuring for SM3.0, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1 and SM7.0
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
Error: gcc is not well formed or produces unusual version details!
Check for a CC environment variable.
Configure failed due to the errors above!
While ? ./configure -clang ? gives me the following error:
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 17 patches:
No patches available
Available Amber 16 patches:
No patches available
AMBER_PREFIX=/Users/kadirozcan/amber16
AMBER_SOURCE=/Users/kadirozcan/amber16
Using the AmberTools miniconda installation in /Users/kadirozcan/amber16/miniconda
version 2.7.13
Error: NVIDIA cuda compilation works only with gnu, Intel, or clang compilers
Configure failed due to the errors above!
How do I solve this configuration issue?
Thank you in advance.
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------------------------------
Message: 3
Date: Mon, 16 Apr 2018 20:00:04 -0400
From: Ashutosh Shandilya <scfbioiitd.gmail.com<mailto:scfbioiitd.gmail.com>>
Subject: [AMBER] convert psf to prmtop
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Message-ID:
<
CAAMUSriRCuyfZNQkNprJNHvcaXs8cE-7zkXe2YNKG9x_g+AWmg.mail.gmail.com<mailto:
CAAMUSriRCuyfZNQkNprJNHvcaXs8cE-7zkXe2YNKG9x_g+AWmg.mail.gmail.com>>
Content-Type: text/plain; charset="UTF-8"
Dear Amber Users
I am trying to convert psf file (which includes water and ions) to convert
to prmtop file to have same number of atoms in amber topology as in psf
file. I tried the following command in parmed
*chamber -top parm99bs0_all.rtf -param par_all36_prot.prm -psf ionized.psf
-crd ionized.pdb*
* -p protein1.prmtop -inpcrd protein1.inpcrd -cmap -verbose*
It gave me error saying
*Action chamber failed*
* UnhandledArgumentWarning: -p protein1.prmtop -inpcrd protein1.inpcrd
-cmap -verbose*
Isn't protein1.prmtop and protein1.inpcrd are output files.
Could you suggest any way to convert psf file to amber prmtop file.
Many thanks.
Ashutosh
------------------------------
Message: 4
Date: Mon, 16 Apr 2018 20:58:16 -0400
From: David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>>
Subject: Re: [AMBER] Configure cuda
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Message-ID:
<
20180417005816.ttyloto6fuy5o3qn.vpn-client-172-16-8-12.rutgers.edu<mailto:
20180417005816.ttyloto6fuy5o3qn.vpn-client-172-16-8-12.rutgers.edu>>
Content-Type: text/plain; charset=utf-8
On Mon, Apr 16, 2018, Kadir Ozcan wrote:
export CUDA_HOME=/Developer/NVIDIA/CUDA-9.0
Be sure you have installed updates at least up to update.8 for
AmberTools17: that is required for CUDA 9.0. (I'm guessing you have
done this, since I think you would have seen a different error message;
but it is best to check.)
cd $AMBERHOME
./configure -cuda gnu
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
What gcc compiler are you using? What is the result of typing "which
gcc"? of typing "gcc -v". If your gcc is /usr/bin/gcc, you are actually
using the clang compiler.
While ? ./configure -clang ? gives me the following error:
Is the above a typo? Can you confirm the exact command you used?
I'd recommend installing gnu compilers from a distribution like
macports. But that doesn't explain the messages you are getting. We
need the information requested above to be of much help.
------------------------------
Message: 5
Date: Mon, 16 Apr 2018 21:06:55 -0400
From: David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>>
Subject: Re: [AMBER] convert psf to prmtop
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Message-ID:
<
20180417010655.nc6fspn4fpbtjkmv.vpn-client-172-16-8-12.rutgers.edu<mailto:
20180417010655.nc6fspn4fpbtjkmv.vpn-client-172-16-8-12.rutgers.edu>>
Content-Type: text/plain; charset=us-ascii
On Mon, Apr 16, 2018, Ashutosh Shandilya wrote:
I am trying to convert psf file (which includes water and ions) to convert
to prmtop file to have same number of atoms in amber topology as in psf
file. I tried the following command in parmed
*chamber -top parm99bs0_all.rtf -param par_all36_prot.prm -psf ionized.psf
-crd ionized.pdb*
* -p protein1.prmtop -inpcrd protein1.inpcrd -cmap -verbose*
This doesn't look like the arguments to the chamber action: type "help
chamber" inside parmed to see the allowable options.
* UnhandledArgumentWarning: -p protein1.prmtop -inpcrd protein1.inpcrd
-cmap -verbose*
As the help page indicates, there are no "-p", "inpcrd", "-cmap" or
"-verbose" flags. (Are you copying from the now-obsolete stand-alone
program called chamber?)
You basically use the first two lines above, then use the "parmout"
action to specify an output prmtop file, and a writeCoordinates action to
specify an ouptut file for the coordinates.
...good luck....dac
------------------------------
Message: 6
Date: Mon, 16 Apr 2018 21:15:47 -0400
From: David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>>
Subject: Re: [AMBER] Regarding AuCl force field
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Message-ID:
<
20180417011547.szniiwt5qgvdcoy3.vpn-client-172-16-8-12.rutgers.edu<mailto:
20180417011547.szniiwt5qgvdcoy3.vpn-client-172-16-8-12.rutgers.edu>>
Content-Type: text/plain; charset=us-ascii
On Mon, Apr 16, 2018, Aashish Bhatt wrote:
I am trying to simulate AuCl complex with protein. I have made Zn++ force
field parameter via MCPB.py method But in that case Zn++ was bound to
protein.
Can I use mcpb.py for AuCl complex also even though it is not bound to any
residue.
Are you referring to AuCl as a solid, somehow interacting with a
protein; is there water around? (Note that AuCl has a tendency to
disproportionate into metallic Au and AuCl3 when in contact with water.)
For such a situation, MCPB won't help: it is designed for situations
where cation and anion dissoicate, and the metal cation is bound to
protein atoms.
...hope this helps....dac
------------------------------
Message: 7
Date: Tue, 17 Apr 2018 06:30:41 +0200
From: FyD <fyd.q4md-forcefieldtools.org<mailto:fyd.q4md-forcefieldtools.org>>
Subject: Re: [AMBER] md simulation of modified nucleotides in RNA
To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
Message-ID:
<
20180417063041.Horde.L86Rkn3I-qlxHTPDTG8i_2R.webmail.u-picardie.fr<mailto:
20180417063041.Horde.L86Rkn3I-qlxHTPDTG8i_2R.webmail.u-picardie.fr>>
Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes
Dear Leila,
Can I use Amber for md simulation of modified nucleotides in RNA?
You might try PyRED at RED Server Dev.
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fq4md-forcefieldtools.org%2FREDServer-Development%2F&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=4P7tm2ijbaN5mDceGijRgdF6VJZsJZKfaF3DCN%2B2gq8%3D&reserved=0
See tutorials:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fq4md-forcefieldtools.org%2FTutorial%2FTutorial-4.php&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=i55DfbTUe1xeyzihcPloDb0P%2FtWil4aHuQSaU699mco%3D&reserved=0
and in particular how to generate molecular fragments from whole
molecule(s):
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fq4md-forcefieldtools.org%2FTutorial%2FTutorial-4.php%232&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=UlSt5d46GZMQllWwicQbL%2FEWL2Bqj8%2BP%2F4OyP%2B%2BvzjU%3D&reserved=0
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fq4md-forcefieldtools.org%2FTutorial%2FTutorial-4.php%2319&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=9VpxWoMMoE%2FYRHl2CPWflv19bZAq60DPcrMjeRBSdz4%3D&reserved=0
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fq4md-forcefieldtools.org%2FTutorial%2FTutorial-4.php%2327&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=8sVbZfHf2Jsfm1TAzKz1yZBdD0m80G3vxrbsfYESj%2BY%3D&reserved=0
In your case you likely have to start from modified RNA
nucleo_s_ide(s) + dimethylphosphate whole molecules to create modified
nucleo_t_ide fragments.
regards, Francois
F.-Y. Dupradeau
---
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------------------------------
Message: 8
Date: Tue, 17 Apr 2018 08:52:35 -0400
From: Jason Swails <jason.swails.gmail.com>
Subject: Re: [AMBER] convert psf to prmtop
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAEk9e3puGjQTs90Lmf_sydtKpxjCe3=ehF4eoNg38+opaUa3yw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
A small additional tip -- you can see an example of how to use the
"chamber" command in parmed by looking at the relevant tests.
Look at $AMBERHOME/AmberTools/test/parmed/chamber/parmed.in for details.
HTH,
Jason
On Mon, Apr 16, 2018 at 9:06 PM, David A Case <david.case.rutgers.edu>
wrote:
On Mon, Apr 16, 2018, Ashutosh Shandilya wrote:
I am trying to convert psf file (which includes water and ions) to
convert
to prmtop file to have same number of atoms in amber topology as in psf
file. I tried the following command in parmed
*chamber -top parm99bs0_all.rtf -param par_all36_prot.prm -psf
ionized.psf
-crd ionized.pdb*
* -p protein1.prmtop -inpcrd protein1.inpcrd -cmap -verbose*
This doesn't look like the arguments to the chamber action: type "help
chamber" inside parmed to see the allowable options.
* UnhandledArgumentWarning: -p protein1.prmtop -inpcrd protein1.inpcrd
-cmap -verbose*
As the help page indicates, there are no "-p", "inpcrd", "-cmap" or
"-verbose" flags. (Are you copying from the now-obsolete stand-alone
program called chamber?)
You basically use the first two lines above, then use the "parmout"
action to specify an output prmtop file, and a writeCoordinates action to
specify an ouptut file for the coordinates.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
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--
Jason M. Swails
------------------------------
Message: 9
Date: Tue, 17 Apr 2018 08:59:02 -0400
From: Maya Hauss <lordofthebhokaral.gmail.com>
Subject: Re: [AMBER] Replica exchange in explicit solvent
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CACG4N+6UH5A91Onuvnb3NgxDO4LZqeXtE0CFYT7pkPFRpuVs=g.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Vincius,
Thank you for your mail. You were right that I had not set the
icnstph flag for the equilibriation. When I include that flag,
the equilibriation fails with the same error as before.
"forrtl: severe (18): too many values for NAMELIST variable"
It must be something wrong with my cpin file, but I cannot
figure out what that might be. I did create a new cpin for the
explicit simulations. I have been trying to titrate HIP, CYS, LYS
and TYR residues on my protein. So the equilibriation currently
fails when I use the cpin generated using following command -
cpinutil.py -p test.prmtop -resnames HIP LYS CYS TYR -igb 2 -o test.cpin
-op test.mod.prmtop
However, it runs successfully when I use the cpin from
cpinutil.py -p test.prmtop -resnames HIP LYS CYS -igb 2 -o test.cpin -op
test.mod.prmtop
Is there a limit on the maximum number of residues that can be allowed to
titrate? Could
that be the reason for my error?
Appreciate your help with this.
Thank you
Maya
On Fri, Apr 13, 2018 at 3:36 PM, Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:
Hello Maya,
The cpin file will not be read unless icnstph=1 or 2, thus it was not read
during your equilibration. The cpin file for a implicit solvent simulation
is not going to be the same as for a explicit solvent simulation. Did you
use cpinutils.py to generate a new cpin for the explicit solvent
simulation? Just for testing, try to run a single simulation with icnstph=2
and without pH-REMD just to see it works.
Best,
Vin?cius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Maya Hauss <lordofthebhokaral.gmail.com>
Sent: Friday, April 13, 2018 3:23:12 PM
To: amber.ambermd.org
Subject: [AMBER] Replica exchange in explicit solvent
Hi,
I have been trying to combine the tutorials for ph replica exchange in
implicit solvent (
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=rkFHJ4EvHOTxPWZG30xGb77vUTAJvbQDCm2p1wIp5v4%3D&reserved=0
3A__jswails.wikidot.com_ph-2Dremd&d=DwICAg&c=
pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&
s=t3Gkpr5qQeV7_VDSF0PD923Fo2KRjqs2rolAbwO5uAQ&e=), and constant ph
simulations in explicit solvent (
https://urldefense.
proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_&d=DwICAg&c=
pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&s=UccR2VU_
W3NDpX4pPiPHHJJZFOC2euDVE665NDel07s&e=
explicit-solvent-constant-ph-md) to perform replica exchange in explicit
solvent.
I used the following input file for my production run
imin=0, irest=1, ntx=5, ntxo = 2
ntpr=1000, ntwx=1000, nstlim=3000,
dt=0.002, ntt=3, tempi=300,
icnstph=2, ntcnstph=100, ntrelax=200,
solvph=8.0, saltcon=0.1, temp0=300.0,
ntc=2, ntf = 2, gamma_ln=1.0, ig=-1, ntp=1,
cut=8, ntb=2, iwrap=1, ioutfm=1,
However, whenever i include the icnstph=2 parameter, I get the following
error
message *"forrtl: severe (18): too many values for NAMELIST variable" *
pointing
to the input cpin file. I did not have any problems using the same cpin
file
for the equilibriation run without the icnstph=2 parameter, or with the
entire imlicit solvent tutorial.I am not sure if I am doing something wrong
in combining the two tutorials. Would appreciate help with this issue. I am
using amber 16 update13.
Maya
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------------------------------
Message: 10
Date: Tue, 17 Apr 2018 21:24:03 +0800 (GMT+08:00)
From: "Huan He" <2010301040026.whu.edu.cn>
Subject: [AMBER] Weight the xyz components of restraints
To: amber.ambermd.org
Message-ID:
<75ed3bde.6b23b.162d3c6cb41.Coremail.2010301040026.whu.edu.cn>
Content-Type: text/plain; charset=UTF-8
Hello! I met some trouble in restraint weight rescently. In page 461 of amber16 mannual, it is known that we can wight the restraint force in x, y, z component by using fxyz options. However, it seems that amber14 is not equipped with this function. How could I do this in amber14. Thankyou!
------------------------------
Message: 11
Date: Tue, 17 Apr 2018 16:20:02 +0200 (CEST)
From: <Lorena.Rosaleny.uv.es>
Subject: Re: [AMBER] Simple normal mode analysis in amber
To: amber.ambermd.org
Message-ID: <2934263533rosaleny.uv.es>
Content-Type: text/plain; charset="UTF-8"
Dear David,
It's not clear exactly what program you tried to compile and execute.
I've attached my version (bench_nm.nab), along with the output from
"./a.out gcn4p1". I hope this helps you find the problem.
Again, since we don't know what output you really got, it's hard to say
whether something is wrong or not. You asked for 0 eigenvectory (eigp),
so you won't get a vecs file in that case.
Thank you very much for your answer. Indeed I used a similar nab script as the one you attached (bench_nm.nab), and as you said my problem was that I was setting eigp the (4th argument in the nmode routine) as 0, and this prevented the vecs file from being created, as I did not ask for any eigenvalue to be computed.
So, in order to get the first 10 normal modes, I changed the following bench_nm.nab script lines:
// get the normal modes:
nmode( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);
to:
// get the normal modes:
nmode( x, 3*m.natoms, mme2, 0, 10, 0.0, 0.0, 0);
Compiled the nab script, and then executed:
/bench_nm.nab gcn4p1 > stdout_nmodes.txt
Finally I got the vecs file with the normal modes on it, and the stout_nmodes.txt file. The stdout_nmodes.txt contained basically what you posted as output for your "./a.out gcn4p1" execution (I copied most of it below). I believe that the reduced masses for each normal mode should be in this txt file. How can I find these reduced masses? Thank you again,
Lorena
stdout_nmodes.txt
----------------------------------------
Reading parm file (gcn4p1.top)
title:
no velocities were found
mm_options: cut=9999.0
mm_options: rgbmax=9999.0
mm_options: ntpr=1
mm_options: nsnb=9999
mm_options: gb=1
mm_options: diel=C
iter Total bad vdW elect nonpolar genBorn frms
ff: 0 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.31e-01
ff: 1 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.28e-01
ff: 2 -3591.04 409.68 -346.17 -2195.72 0.00 -1458.84 3.09e-01
ff: 3 -3591.10 409.63 -346.18 -2195.72 0.00 -1458.83 1.34e-01
ff: 4 -3591.11 409.62 -346.18 -2195.72 0.00 -1458.83 1.01e-01
ff: 5 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0039677
For alpha = 0.00000 energy = -3591.1212131189
For alpha = 1.00000 energy = -3591.1325809770
For alpha = 0.99418 energy = -3591.1325813675
For alpha = 0.99423 energy = -3591.1325813675
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0002543
For alpha = 0.00000 energy = -3591.1325813675
For alpha = 1.00000 energy = -3591.1326022869
For alpha = 2.00000 energy = -3591.1325837201
For alpha = 1.02272 energy = -3591.1326022968
For alpha = 1.02202 energy = -3591.1326022970
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000180
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000000
ff: 5 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
Energy = -3.5911326023e+03
RMS gradient = 1.6327027163e-12
dysev time = 60.62 seconds
- Thermochemistry -
Temperature: 298.150
Pressure: 1.000
Mass: 7506.824
Principal moments of inertia in amu-A**2:
289887.38 1439066.88 1492272.08
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.000 0.000 0.000
Zero-point vibrational energy: 5735.169
freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 2507.471 2161.002 2724.346
translational: 0.888 2.979 52.555
rotational: 0.888 2.979 52.272
vibrational: 6096.827 2155.044 2619.518
ff energy: -3591.133
1 -0.000
2 -0.000
3 -0.000
4 -0.000
5 0.000
6 0.000
7 3.220 0.592 1.986 10.254
8 3.684 0.592 1.986 9.987
9 4.251 0.592 1.986 9.703
10 5.352 0.592 1.986 9.246
11 6.351 0.592 1.986 8.906
12 7.373 0.592 1.986 8.609
13 7.954 0.592 1.986 8.459
14 8.489 0.592 1.986 8.329
.
.
.
3245 3352.525 4.793 0.000 0.000
3246 3354.907 4.796 0.000 0.000
3247 3356.688 4.799 0.000 0.000
3248 3364.660 4.810 0.000 0.000
3249 3688.735 5.274 0.000 0.000
3250 3688.768 5.274 0.000 0.000
3251 3692.834 5.279 0.000 0.000
3252 3692.837 5.279 0.000 0.000
-------------------------------------------------
Date: Mon, 16 Apr 2018 08:59:11 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Simple normal mode analysis in amber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<20180416125911.ny2b3z65rmzm33dr.vpn-client-172-16-8-12.rutgers.edu>
Content-Type: text/plain; charset="us-ascii"
On Mon, Apr 16, 2018, Lorena.Rosaleny.uv.es wrote:
I'd like to calculate normal modes for a simple protein, and
I'm trying to use the approach suggested by David Case, with
the code shown on Amber17 manual page 833 (section 39.4 Second
derivatives and normal modes). I downloaded the gcn4p1.mc.pdb from the
$AMBEHROME/AmberTools/benchmarks/nab/benchamarks/nab/ directory but got
this when executing:
It's not clear exactly what program you tried to compile and execute.
I've attached my version (bench_nm.nab), along with the output from
"./a.out gcn4p1". I hope this helps you find the problem.
I also tried to use the script bench_nr.nab with the
gcn4p1 example. I used the pdb, top and x files from
$AMBEHROME/AmberTools/benchmarks/nab/benchamarks/nab/. I added to the
end of the script the same line that is described in the manual to
calculate normal modes ( nmodes( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0,
0)), but I got a stdout that didn't seem to contain the full information
on the normal modes (reduced mass, frequency and displacement vectors
for each atom). I was expecting a vecs file, but didn't get one.
Again, since we don't know what output you really got, it's hard to say
whether something is wrong or not. You asked for 0 eigenvectory (eigp),
so you won't get a vecs file in that case.
..good luck....dac
-------------- next part --------------
Reading parm file (gcn4p1.top)
title:
no velocities were found
mm_options: cut=9999.0
mm_options: rgbmax=9999.0
mm_options: ntpr=1
mm_options: nsnb=9999
mm_options: gb=1
mm_options: diel=C
iter Total bad vdW elect nonpolar genBorn frms
ff: 0 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.31e-01
ff: 1 -3591.04 409.69 -346.17 -2195.72 0.00 -1458.84 3.28e-01
ff: 2 -3591.04 409.68 -346.17 -2195.72 0.00 -1458.84 3.09e-01
ff: 3 -3591.10 409.63 -346.18 -2195.72 0.00 -1458.83 1.34e-01
ff: 4 -3591.11 409.62 -346.18 -2195.72 0.00 -1458.83 1.01e-01
ff: 5 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.12 409.60 -346.18 -2195.73 0.00 -1458.82 4.65e-02
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0039677
For alpha = 0.00000 energy = -3591.1212131189
For alpha = 1.00000 energy = -3591.1325809770
For alpha = 0.99418 energy = -3591.1325813675
For alpha = 0.99423 energy = -3591.1325813675
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
ff: 2 -3591.13 409.57 -346.06 -2196.17 0.00 -1458.48 3.30e-03
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0002543
For alpha = 0.00000 energy = -3591.1325813675
For alpha = 1.00000 energy = -3591.1326022869
For alpha = 2.00000 energy = -3591.1325837201
For alpha = 1.02272 energy = -3591.1326022968
For alpha = 1.02202 energy = -3591.1326022970
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
ff: 3 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 4.55e-05
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000180
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
ff: 4 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.31e-06
adding 0.00000 to diagonal of the hessian
rms of search direction: 0.0000000
ff: 5 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
iter Total bad vdW elect nonpolar genBorn frms
ff: 1 -3591.13 409.56 -346.05 -2196.21 0.00 -1458.43 1.63e-12
Energy = -3.5911326023e+03
RMS gradient = 1.6327027163e-12
dysev time = 10.53 seconds
- Thermochemistry -
Temperature: 298.150
Pressure: 1.000
Mass: 7506.824
Principal moments of inertia in amu-A**2:
289887.38 1439066.88 1492272.08
Rotational symmetry number is 1
Assuming classical behavior for rotation
Rotational temperatures: 0.000 0.000 0.000
Zero-point vibrational energy: 5735.169
freq. E Cv S
cm**-1 kcal/mol cal/mol-K cal/mol-K
Total: 2507.471 2161.002 2724.346
translational: 0.888 2.979 52.555
rotational: 0.888 2.979 52.272
vibrational: 6096.827 2155.044 2619.518
ff energy: -3591.133
1 -0.000
2 -0.000
3 -0.000
4 -0.000
5 -0.000
6 0.000
7 3.220 0.592 1.986 10.254
8 3.684 0.592 1.986 9.987
9 4.251 0.592 1.986 9.703
10 5.352 0.592 1.986 9.246
11 6.351 0.592 1.986 8.906
12 7.373 0.592 1.986 8.609
13 7.954 0.592 1.986 8.459
14 8.489 0.592 1.986 8.329
15 9.109 0.592 1.986 8.189
16 9.724 0.592 1.986 8.060
17 10.093 0.592 1.985 7.986
18 11.369 0.592 1.985 7.749
19 11.499 0.592 1.985 7.727
20 12.147 0.592 1.985 7.618
21 12.154 0.592 1.985 7.617
22 12.805 0.592 1.985 7.513
23 13.339 0.592 1.985 7.432
24 13.536 0.592 1.985 7.403
25 13.610 0.592 1.985 7.392
26 14.180 0.592 1.985 7.311
27 14.504 0.592 1.985 7.266
...
3249 3688.735 5.274 0.000 0.000
3250 3688.768 5.274 0.000 0.000
3251 3692.834 5.279 0.000 0.000
3252 3692.837 5.279 0.000 0.000
-------------- next part --------------
// Try some newton-raphson minimization
molecule m;
float x[dynamic], v[dynamic];
float fret;
// Create a molecule from a pdb file and a force-field parameter file.
m = getpdb( argv[2] + ".mc.pdb");
allocate x[ 3*m.natoms ];
allocate v[ 3*m.natoms ];
readparm( m, argv[2] + ".top" );
getxv( argv[2] + ".mc.x", m.natoms, fret, x, v );
// Initialize molecular mechanics..
mm_options("cut=9999.0, rgbmax=9999.0, ntpr=1, nsnb=9999, gb=1, diel=C" );
mme_init(m, NULL, "::ZZZZ", x, NULL);
// conjugate gradient minimization
conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 2000 );
// Newton-Raphson minimization
newton( x, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 6 );
nmode(x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0 );
// mme2_timer();
--
Lorena E. Rosaleny Peralvo, Senior Postdoctoral Researcher
Telf. +0034 963 544 418
Instituto de Ciencia Molecular
Universitat de Val?ncia
c/ Catedr?tico Jos? Beltr?n Mart?nez n? 2
46980 Paterna (Val?ncia)
SPAIN
------------------------------
Message: 12
Date: Tue, 17 Apr 2018 14:49:47 +0000
From: "Cruzeiro,Vinicius Wilian D" <vwcruzeiro.ufl.edu>
Subject: Re: [AMBER] Replica exchange in explicit solvent
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<BN6PR2201MB1284986E2BBB23356671EA13D1B70.BN6PR2201MB1284.namprd22.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello Maya,
Yes, there is a limit in the total number of residues. If you want, you may alter the following block at $AMBERHOME/src/pmemd/src/constantph.F90 and recompile pmemd.
! Limits on the sizes of the data structures
#define MAX_TITR_RES 50
#define MAX_TITR_STATES 200
#define MAX_ATOM_CHRG 1000
#define MAX_H_COUNT 4
However, it is advisable to reduce the number of residues in your cpin file rather than doing this. Increasing the number of residues reduces the computational efficiency of your simulation. In general, people only consider the residues of interest for titration at a given value of pH (or pH range) instead of titrating all possible residues. You may run a short simulation titrating all just to check which residues are important to you.
I hope this helps,
All the best,
Vin?cius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Maya Hauss <lordofthebhokaral.gmail.com>
Sent: Tuesday, April 17, 2018 8:59:02 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Replica exchange in explicit solvent
Dear Vincius,
Thank you for your mail. You were right that I had not set the
icnstph flag for the equilibriation. When I include that flag,
the equilibriation fails with the same error as before.
"forrtl: severe (18): too many values for NAMELIST variable"
It must be something wrong with my cpin file, but I cannot
figure out what that might be. I did create a new cpin for the
explicit simulations. I have been trying to titrate HIP, CYS, LYS
and TYR residues on my protein. So the equilibriation currently
fails when I use the cpin generated using following command -
cpinutil.py -p test.prmtop -resnames HIP LYS CYS TYR -igb 2 -o test.cpin
-op test.mod.prmtop
However, it runs successfully when I use the cpin from
cpinutil.py -p test.prmtop -resnames HIP LYS CYS -igb 2 -o test.cpin -op
test.mod.prmtop
Is there a limit on the maximum number of residues that can be allowed to
titrate? Could
that be the reason for my error?
Appreciate your help with this.
Thank you
Maya
On Fri, Apr 13, 2018 at 3:36 PM, Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:
Hello Maya,
The cpin file will not be read unless icnstph=1 or 2, thus it was not read
during your equilibration. The cpin file for a implicit solvent simulation
is not going to be the same as for a explicit solvent simulation. Did you
use cpinutils.py to generate a new cpin for the explicit solvent
simulation? Just for testing, try to run a single simulation with icnstph=2
and without pH-REMD just to see it works.
Best,
Vin?cius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Maya Hauss <lordofthebhokaral.gmail.com>
Sent: Friday, April 13, 2018 3:23:12 PM
To: amber.ambermd.org
Subject: [AMBER] Replica exchange in explicit solvent
Hi,
I have been trying to combine the tutorials for ph replica exchange in
implicit solvent (
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=rkFHJ4EvHOTxPWZG30xGb77vUTAJvbQDCm2p1wIp5v4%3D&reserved=0
3A__jswails.wikidot.com_ph-2Dremd&d=DwICAg&c=
pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&
s=t3Gkpr5qQeV7_VDSF0PD923Fo2KRjqs2rolAbwO5uAQ&e=), and constant ph
simulations in explicit solvent (
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__urldefense%26d%3DDwIGaQ%26c%3DpZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM%26r%3DLIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc%26m%3DbNv4yrBApZuh4XxAjNquC0YM9sF4rh0CmoqcbOU_xL8%26s%3DtLM1nhl81jCpV9jqpKOAyyUBi9bnwwX850VifCNZArw%26e&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398695615&sdata=mNfWY048tjmSm5ozals9m0SPUwsDhFQvQxA%2FItXYgW8%3D&reserved=0=.
proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_&d=DwICAg&c=
pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&s=UccR2VU_
W3NDpX4pPiPHHJJZFOC2euDVE665NDel07s&e=
explicit-solvent-constant-ph-md) to perform replica exchange in explicit
solvent.
I used the following input file for my production run
imin=0, irest=1, ntx=5, ntxo = 2
ntpr=1000, ntwx=1000, nstlim=3000,
dt=0.002, ntt=3, tempi=300,
icnstph=2, ntcnstph=100, ntrelax=200,
solvph=8.0, saltcon=0.1, temp0=300.0,
ntc=2, ntf = 2, gamma_ln=1.0, ig=-1, ntp=1,
cut=8, ntb=2, iwrap=1, ioutfm=1,
However, whenever i include the icnstph=2 parameter, I get the following
error
message *"forrtl: severe (18): too many values for NAMELIST variable" *
pointing
to the input cpin file. I did not have any problems using the same cpin
file
for the equilibriation run without the icnstph=2 parameter, or with the
entire imlicit solvent tutorial.I am not sure if I am doing something wrong
in combining the two tutorials. Would appreciate help with this issue. I am
using amber 16 update13.
Maya
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------------------------------
Message: 13
Date: Tue, 17 Apr 2018 10:50:15 -0400
From: David A Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Simple normal mode analysis in amber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<20180417145015.j7amzrbgzqp7gd3c.vpn-client-172-16-8-12.rutgers.edu>
Content-Type: text/plain; charset=us-ascii
On Tue, Apr 17, 2018, Lorena.Rosaleny.uv.es wrote:
Finally I got the vecs file with the normal modes on it, and the
stout_nmodes.txt file. The stdout_nmodes.txt contained basically what
you posted as output for your "./a.out gcn4p1" execution (I copied most
of it below). I believe that the reduced masses for each normal mode
should be in this txt file. How can I find these reduced masses? Thank
you again,
Amber doesn't compute reduced masses for normal modes. I guess you
would have to write a script yourself to do this: the masses are in the
prmtop file, and the eigenvectors are in the vecs file.
Note that cpptraj can read in eigenvector files and work with them.
Perhaps that might do what you really want. That is, why do you want to
get the reduced mass? (One reason we don't compute these is that I've
never needed it, and no one else has ever requested it, as far as I can
remember.)
....dac
------------------------------
Message: 14
Date: Tue, 17 Apr 2018 17:12:58 +0200
From: Raimon Fabregat <raimon.fabregat.epfl.ch>
Subject: [AMBER] QMMM Replica exchange with TeraChem
To: amber.ambermd.org
Message-ID: <b88653f4-4c27-1d39-c5f1-f7cd19f990a6.epfl.ch>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear all,
I am trying to launch a simulation with hamiltonian replica exchange
where TeraChem (in gpu) should be in charge to do the QM part, but the
simulation crashes at the start with this error:
Running multisander version of sander Amber16
??? Total processors =???? 2
??? Number of groups =???? 2
Fatal error in MPI_Lookup_name: Invalid service name (see
MPI_Publish_name), error stack:
MPI_Lookup_name(161): MPI_Lookup_name(service="terachem_port.001",
MPI_INFO_NULL, port=0x17f91d00) failed
MPI_Lookup_name(136): fail failed
MPID_NS_Lookup(73)..: Lookup failed for service name terachem_port.001
First of all, do you know if it is possible to do what I want to do?
If so I will detail more the problem to see what I did wrong.
Thanks a lot!
Best,
Raimon
------------------------------
Message: 15
Date: Tue, 17 Apr 2018 11:40:14 -0400
From: David Cerutti <dscerutti.gmail.com>
Subject: [AMBER] How fast is Amber's new GPU code? Are CPUs ever
coming back?
To: AMBER Mailing List <amber.ambermd.org>
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And now for a public service announcement...
Recently on the list people have been writing in asking about the speed of
pmemd, of its GPU acceleration, which simulation program to use, and so
forth. One newcomer even asked whether the GPU code is faster than sander,
and reading between the lines I can see a PI or two wondering whether the
Amber package, as opposed to the freely distributed AmberTools, is worth
the investment. While I'm not here to advertise per se, I will offer the
following observations, which should help anyone trying to understand the
current state of the field, how fast is Amber, and where the technology is
taking us.
Elmar Krieger, perhaps my European doppleganger for the way he ebbs from
force fields to simulation methodology and back, published a fascinating
article back in 2015 showing how they took a single Core i7-5960X Haswell
processor and pushed the dihydrofolate reductase (DHFR, explicit water
molecules) simulation throughput from a humdrum 7.5 ns / day reference (1
fs time step, long cutoff) to run more than 20x faster through a series of
approximations that they demonstrate to be safe:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fonlinelibrary.wiley.com%2Fdoi%2Ffull%2F10.1002%2Fjcc.23899&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398705623&sdata=1Fw31nftt46tBidnIkO0Pqd7PeRF2ntnUEp%2FzJw8%2BoE%3D&reserved=0
This is a big achievement--given the way they talk about AVX instructions
and their proximity to the GROMACS folks I'm going to assume they coded it
'right' and can't get their YASARA program significantly faster under the
same approximations on the same hardware. The paper says "a single Core
i7-5960X" but that's a capital C--they use all eight cores, 16 threads, of
the hyperthreaded Core i7 processor, and I am going to assume that they're
not turbo-boosting because their program is running consistently enough
that there's not much opportunity for the chip to safely ramp up the clock
speed on any particular core.
First, let's compare the nuts and bolts of YASARA to what Amber's primary
simulation engine, pmemd, does. We have something almost identical to DHFR
in terms of atom counts and run conditions (most significantly, PME and
8.0A cutoff): we call it JAC and you can find it on our benchmarks page:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Fgpus%2Fbenchmarks.htm%23Benchmarks&data=02%7C01%7CKadir.Ozcan%40jefferson.edu%7C514ae750bba944ed9a8c08d5a49581ca%7C55a89906c710436bbc444c590cb67c4a%7C0%7C0%7C636595884398705623&sdata=x8s3sCtTBlLGEUNWlqGNhSHSskF%2F%2BtlAJ2ozWdHV3hw%3D&reserved=0
Off the cuff, YASARA looks like it might be a bit faster than our pmemd CPU
code, but not tremendously so until they start invoking more drastic
approximations (we kind of part ways once they get to the lime green line
on Figure 8, when we use heavy hydrogens to get to a 4fs time step and they
use LINCS with multiple time steps). We maintain an 'air tight' pair list,
which guarantees that every interaction within the stated cutoff is going
to be counted (there was a kerfuffle on the listserv a few months back when
I said there was a chink in the armor with Amber16, but we've patched
that). YASARA takes a GROMACS-like approach with what they call a "sloppy"
pair list, which one can reasonably argue is no more an approximation than
hard truncation of vdW interactions or the tail of the erfc(r)/r function
in PME. Krieger and Vriend then get another impressive boost from atomic
instructions (for those unfamiliar, this is a fundamental problem of
parallel computing, and works like a library checkout system so that common
pieces of memory can only have one thread operating on them at a time).
The additional boost that they then get from a more advanced method for
ensuring that threads don't negate one another's results is small, but they
get another big jump by writing their program to avoid the need to worry
about threads crossing paths in the first place. Newer vector instruction
sets add a little more, and their "densostat," which approximates the
effect of a barostat but merely works to keep the simulation box size where
the user thinks it should be as opposed to where the Newtonian physics
would actually take it, is an 8% boost, comparable to the effect we see for
invoking or removing a virial calculation.
Now back to logistics. There are a couple of facts pertinent to the
questions on the listserv that are not in the paper: the price of that
high-performance Haswell processor (currently about $900, on clearance as
it has been succeeded by the new Skylake line), and the power envelope
(140W). The price of the modern equivalent Core i9-7960X Skylake is about
$1400. Skylake doubles the number of cores and threads, but the clock
speed is back down, the cache is not that much bigger, and the power
envelope has gone up to 165W. Tick, tock, tick, tock. I'm just going to
estimate that on a new Skylake Krieger and colleagues might be able to get
DHFR to run at 250ns / day. As stated above, the approximations made by
pmemd and YASARA are not comparable, and not everything that Krieger does
on a CPU will map to a GPU although a good portion of it will. But let's
go ahead and compare the results to our GTX-1080Ti benchmarks. The new
pmemd.cuda is somewhat faster than the Amber16 code, and I have more
optimizations in my own branch, working within our original set of
approximations and running the JAC benchmark at 730ns / day. A GTX-1080Ti
cost $700 when it was new, and while the forthcoming GPUs will almost
certainly be more expensive thanks to the diligence of coin farmers, I
don't expect the price of a new Volta-like GTX to crest much above $1100.
Let's just stick with last year's model, though.
The GTX-1080Ti is a 250W card, but on the JAC/DHFR benchmarks it doesn't
ramp up completely (system isn't big enough), so the power consumption is
around 175W. The GPU is therefore beating the CPU by a factor of nearly 3
in speed, for half the cost, and only slightly more electricity consumption
(running a 250W GPU round the clock for a year at 0.12 cents per kW/hr will
run you about $260). As I said, JAC can't fully occupy the GPU--bigger
systems run up to 30% more effectively, with the throughput reaching a
plateau for systems about 3-4 times the size of JAC. In contrast, Krieger
shows that the CPU offers nearly linear returns as a function of system
size, with slight degradation due to the O(N log N) property of the FFT.
(The FFT scaling is a weak effect on GPUs, which in fact do FFTs very
efficiently and reach peak efficiency in the FFT at about the same time
they reach peak efficiency in other aspects of the algorithm.) So on bigger
systems the GPU will retain its advantage in terms of power consumption and
grow its lead substantially in terms of throughput. Of course, if we were
to invoke some of the approximations that Krieger shows on the CPU, our GPU
performance would likewise benefit.
As I said, I'm not doing this to advertise, and I'm certainly not doing it
to call out Krieger and Vriend for their statement that the technological
revolution that took computational science to GPUs may be shifting back to
CPUs. There is truth to that statement, and Elmar has done some fabulous
work which I also admire for the way he thought out of the box and ran his
dynamics without a Verlet pair list (have a look at mdgx). However, it
underscores the current state of things: while CPUs are making impressive
gains of their own, GPUs retain a considerable lead in terms of simulation
speed and power consumption. As long as NVIDIA continues to let us use GTX
for scientific applications, the GPUs have a considerable cost advantage as
well.
Another way to look at this is that CPUs devote a lot of their silicon to
cache, a dustbin of information that, at some time in the last few hundred
thousand transactions, was hauled in from RAM. GPUs, by contrast, devote
much more of their silicon to arithmetic units, have very little cache, and
run at about half the clock speed of a CPU. Aside from those differences,
the lithography and circuits are pretty much the same. It pretty well
explains the differences in power consumption and throughput when you just
look at what each device is doing with the silicon. In that sense, I would
expect GPUs to maintain their logistical advantages over CPUs for
compute-intensive operations.
In terms of programming, one must be mindful of the scarcity of cache on
each GPU "core" (the streaming multi-processor, of which the new Volta
architecture has 80 on an immense 81 cm2 die). But, I feel that in their
paper Krieger and Vriend have touched on another aspect of the computing
revolution that is now flowing back to CPUs:
"Although compilers could in theory do [Advanced Vector Extensions]
automatically, it does not work well enough in practice. Instead, the
developer must write code that explicitly uses these instruction sets,
either by programming directly in assembly language, or by using
'intrinsics,' small C/C++ functions that operate on vector data types and
map almost directly to the corresponding assembly instructions, so that the
compiler has an easy job... one needs to rewrite or at least adapt the code
for each SIMD instruction set (and almost every new CPU comes with
additional SIMD instructions)."
For a long time, GPU programming was considered a barrier that saddled the
scientific computing revolution on the backs of a group of people who might
not be computer science geniuses but at least had invested something to
learn an advanced language. In practice, the threshold for CUDA
programming is to understand that whatever instructions one writes will be
executed by some combination of 32 threads (32-way SIMT), how to manage a
very small cache effectively, and how big the GPU really is. Otherwise,
CUDA is more or less like C. The computer scientists behind GPUs work in
close concert with software developers to provide solutions to fundamental
parallel computing problems like atomic memory transactions and thread
synchronization, and the innovations have been truly impressive. The
impetus may now be on Intel and other chip makers to provide compiler
support for C- and Fortran-level programming in ways that effectively
utilize vectorization and all cores of these increasingly multi-core CPUs.
The good, and the bad, of the GPU computing revolution is returning to CPUs
themselves. The rosiest future I can foresee is one in which there are
multiple stages between the single-core CPUs of 2000 and the GPUs of today,
where we can all select our price points, the transitions for coding are
incremental, and the device distinctions boil down to how much of the
silicon is for math or short-term memory. Until then, please just know
that Amber is as fast as we can make it go, and for anyone interested in
undertaking a significant MD project it is worthwhile to buy into the GPU
power offered with the licensed version.
------------------------------
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End of AMBER Digest, Vol 2264, Issue 1
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Received on Tue Apr 17 2018 - 12:30:03 PDT
