Re: [AMBER] AMBER Digest, Vol 2349, Issue 1

From: Stejskal, Lenka <lenka.stejskal.15.ucl.ac.uk>
Date: Tue, 17 Jul 2018 14:46:17 +0000

Hi Dan,


Thank you for your answer. It was most helpful.


I was wondering whether there is a way to calculate the fraction contribution of each eigenvector to the total motion for individual trajectories from the matrix created using multiple trajectories.


Thank you


Lenka



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AMBER Mailing List Digest

Today's Topics:

   1. Re: setting ionic strength in leap (Kris Feher)
   2. Error in MCPB.py step 2 (dhaval patel)
   3. Amber16 to Amber18 upgrade? (Hirdesh Kumar)
   4. Re: Cannot run pdb4amber (Alen Ahmetovic)
   5. Re: Error in MCPB.py step 2 (Pengfei Li)
   6. Re: Amber16 to Amber18 upgrade? (Pengfei Li)
   7. Re: PCA multiple trajectories for mutants and wild type
      (Daniel Roe)
   8. peptide bond restraints (lucrecia bogado)
   9. Re: peptide bond restraints (Wesley Michael Botello-Smith)
  10. translational diffusion coefficient from MSD (Kris Feher)
  11. Re: peptide bond restraints (Carlos Simmerling)
  12. Reduced GPU Performance (Midhun K Madhu)
  13. Fwd: issues with accelerated MD in chloroform (Chetna Tyagi)
  14. Re: Reduced GPU Performance (Matias Machado)
  15. Single Point Calculation on trajectory (Raimon Fabregat)
  16. Per-residue energy decomposition by MMPBSA.pl (Syeda)
  17. convert trajectories files in AMBER (Chhaya Singh)
  18. Re: convert trajectories files in AMBER
      (Charles-Alexandre Mattelaer)
  19. Re: peptide bond restraints (lucrecia bogado)
  20. Re: peptide bond restraints (Carlos Simmerling)
  21. Re: Reduced GPU Performance (Ross Walker)


----------------------------------------------------------------------

Message: 1
Date: Thu, 12 Jul 2018 19:02:30 +0000 (UTC)
From: Kris Feher <kris.feher.yahoo.com>
Subject: Re: [AMBER] setting ionic strength in leap
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <743409151.3024727.1531422150242.mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8

 Dear George,thanks for the references. In any case, it is probably useful to check how the ion distribution is changing over time and maybe discard the initial part where it has not yet reached some sort of equilibrium. As for the size of the box, I will first see if recalculation of experimental data, translational diffusion coefficients from NMR, is affected.Kris


    On Saturday, July 7, 2018, 6:35:08 AM GMT+2, George M. Giambasu <giambasu.gmail.com> wrote:

 Here are few further points to consider when trying to reach a desired
salt concentration in nucleic acids MD simulations:

- the resulting salt concentration after equilibration will be different
from any initial guess, and so, in order to reach a desired
concentration you will want to iteratively change the composition of
your system and equilibrate (here is an example:
http://dx.doi.org/10.1021/jp306598y).

- equilibration of ions and water takes a long time: tens of nanoseconds
for simple helical nucleic acids and at least one order of magnitude
more for cases where ions might bind in cavities.
http://www.pnas.org/content/101/41/14771 is a good starting point.

- imposing specific solution salt conditions refers to maintaining a
specific *bulk* salt concentration, that is the ion concentration in
regions remote from the nucleic acid solute where the local density of
ions is not perturbed by the presence of the nucleic acid.

- typical simulation boxes (having clearances of 10-15 Ang.) are not
able to model a solution bulk, as one has to go *at least* 25 Angstroms
away from the nucleic acid surface to reach the bulk. So, if you want
your your simulation to reflect specific salt conditions (that can be
replicated experimentally) you better choose a large enough box (see
more here: https://doi.org/10.1016/j.bpj.2014.01.021 ,
https://doi.org/10.1016/j.jmb.2009.05.071).


best,

George



~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. George M. Giambasu, Ph.D.
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Room 308E Piscataway,
NJ 08854, USA
giambasu.rutgers.edu
giambasu.gmail.com
rci.rutgers.edu/~giambasu
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


------------------------------

Message: 2
Date: Fri, 13 Jul 2018 01:06:06 +0530
From: dhaval patel <pateldhaval.in.gmail.com>
Subject: [AMBER] Error in MCPB.py step 2
To: amber.ambermd.org
Message-ID:
        <CAHLi5TXEc5fsiiW=LXxp0fBuhSFUj2KYDm=mTkwf1wb8KioJDA.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Dear All,

I am facing problem while executing MCPB.py program at 2 step i.e.
MCPB.py -i xyz.in -s 2


The error is stated below:

Atoms which has changed the atom types: [2501, 2545]
155-RUX.2501-N3 : n2 --> Y1
156-RU.2545-RU : RU --> M1
==================Using the Seminario method to solve the problem.
Traceback (most recent call last):
  File "/home/dhaval/Desktop/amber18//bin/MCPB.py", line 662, in <module>
    fcfchkf, fclogf, g0x, scalef, bondfc_avg, anglefc_avg)
  File
"/home/dhaval/Desktop/amber18/lib/python2.7/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
line 729, in gene_by_QM_fitting_sem
    crds = get_crds_from_fchk(chkfname, len(atids))
  File
"/home/dhaval/Desktop/amber18/lib/python2.7/site-packages/pymsmt/mol/gauio.py",
line 398, in get_crds_from_fchk
    raise pymsmtError('The coordinates number in fchk file are not
consistent '
pymsmt.exp.pymsmtError

Any suggestions?


Sincerely yours,
Dhaval Patel | PhD
The M. S. University of Baroda, Vadodara.
Lab: Biophysics & Structural Biology,
Indian Institute of Advanced Research,
Gujarat, INDIA. +91 9925450504
pateldhaval.in.gmail.com; dhaval.iiar.res.in


------------------------------

Message: 3
Date: Thu, 12 Jul 2018 15:46:13 -0500
From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Subject: [AMBER] Amber16 to Amber18 upgrade?
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAPKknGryUPeTaK816vrTuUmamkgaMBJQLoxm9yeJvUJ564cZ5Q.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

I have license to Amber16. Can I upgrade to Amber18 with the same license ?

Thanks,
Hirdesh
*?*


------------------------------

Message: 4
Date: Thu, 12 Jul 2018 16:56:58 -0400
From: Alen Ahmetovic <alen2.mail.usf.edu>
Subject: Re: [AMBER] Cannot run pdb4amber
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAJ2PjxjV_LfVvB+fObfLcZ1mJBweeDGmVC4La1DJ=Ux2Eoic5A.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Yes, I messed up the syntax, so I tried it again and it worked! Thanks

On Thu, Jul 12, 2018 at 12:37 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:

> have you tried to "source amber.sh" yet?
>
> Hai
>
> On Thu, Jul 12, 2018 at 12:27 AM, Alen Ahmetovic <alen2.mail.usf.edu>
> wrote:
>
> > Hey everyone, I've been having trouble with pdb4amber to run. I've looked
> > through the forum and referring to dac's response to one person who had
> the
> > same problem, I have reinstalled amber to accept miniconda installation a
> > few months ago, and when I type the command "$AMBERHOME/bin/pdb4amber"
> the
> > following script comes up:
> > __________________________________
> >
> > /Users/alenahmetovic/Research/amber16/bin/pdb4amber source amber.sh
> >
> > Traceback (most recent call last):
> >
> > File "/Users/alenahmetovic/Research/amber16/bin/pdb4amber", line 6, in
> > <module>
> >
> > from pdb4amber import pdb4amber
> >
> > ImportError: No module named pdb4amber
> > __________________________________
> >
> > When trying to open pdb4amber by manually going into the folder and
> opening
> > by right-clicking on the program and then Open--> give permission to
> open,
> > the following text pops up:
> > _________________________________
> >
> > Alens-MacBook-Pro:~ alenahmetovic$
> > /Users/alenahmetovic/Research/amber16/bin/pdb4amber ; exit;
> >
> > Traceback (most recent call last):
> >
> > File "/Users/alenahmetovic/Research/amber16/bin/pdb4amber", line 6, in
> > <module>
> >
> > from pdb4amber import pdb4amber
> >
> > ImportError: No module named pdb4amber
> >
> > logout
> >
> > Saving session...
> >
> > ...copying shared history...
> >
> > ...saving history...truncating history files...
> >
> > ...completed.
> >
> > Deleting expired sessions...9 completed.
> >
> >
> > [Process completed]
> >
> > _________________________________
> >
> >
> >
> > This is the result when I check for updates:
> >
> > _______________________________
> >
> > $AMBERHOME/update_amber --check-updates
> >
> > Checking for available patches online. This may take a few seconds...
> >
> >
> > Available AmberTools 17 patches:
> >
> >
> > update.9 (modifies sander)
> >
> > Released on May 21, 2018 (written by Vinicius Wilian D. Cruzeiro)
> >
> > Description:
> >
> > Adds an error message when users run REMD and the box sizes are not the
> > same across all replicas.
> >
> >
> > update.10 (modifies sander)
> >
> > Released on July 07, 2018 (written by Vinicius Wilian D. Cruzeiro)
> >
> > Description:
> >
> > Corrects REMD error trap for different box sizes to account for
> > non-periodic systems.
> > _______________________________
> >
> > I am assuming since neither update mentions anything for pdb4amber, I
> have
> > the most current version? How would I go about solving this? I have
> checked
> > my sub-folders, and do have miniconda.
> >
> > Finally, from the Amber manual: "This is a list of packages that
> AmberTools
> > will install if user chose ?yes?: python2.7, numpy, scipy, cython,
> ipython,
> > notebook, matplotlib.", the only package that was NOT installed was
> > matplotlib. Not sure if that helps or not.
> >
> > Appreciate any insight to this, thanks.
> > _______________________________________________
> > 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: 5
Date: Thu, 12 Jul 2018 17:22:43 -0400
From: Pengfei Li <ambermailpengfei.gmail.com>
Subject: Re: [AMBER] Error in MCPB.py step 2
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <DBC81E28-951D-4E48-8EB1-AC9A0860AD7E.gmail.com>
Content-Type: text/plain; charset=utf-8

Hi Dhaval,

It says the number of atoms in your fchk file doesn?t match the number of atoms in the small PDB file. So there may be a mismatch there.

Hope it helps,
Pengfei

> On Jul 12, 2018, at 3:36 PM, dhaval patel <pateldhaval.in.gmail.com> wrote:
>
> Dear All,
>
> I am facing problem while executing MCPB.py program at 2 step i.e.
> MCPB.py -i xyz.in -s 2
>
>
> The error is stated below:
>
> Atoms which has changed the atom types: [2501, 2545]
> 155-RUX.2501-N3 : n2 --> Y1
> 156-RU.2545-RU : RU --> M1
> ==================Using the Seminario method to solve the problem.
> Traceback (most recent call last):
> File "/home/dhaval/Desktop/amber18//bin/MCPB.py", line 662, in <module>
> fcfchkf, fclogf, g0x, scalef, bondfc_avg, anglefc_avg)
> File
> "/home/dhaval/Desktop/amber18/lib/python2.7/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
> line 729, in gene_by_QM_fitting_sem
> crds = get_crds_from_fchk(chkfname, len(atids))
> File
> "/home/dhaval/Desktop/amber18/lib/python2.7/site-packages/pymsmt/mol/gauio.py",
> line 398, in get_crds_from_fchk
> raise pymsmtError('The coordinates number in fchk file are not
> consistent '
> pymsmt.exp.pymsmtError
>
> Any suggestions?
>
>
> Sincerely yours,
> Dhaval Patel | PhD
> The M. S. University of Baroda, Vadodara.
> Lab: Biophysics & Structural Biology,
> Indian Institute of Advanced Research,
> Gujarat, INDIA. +91 9925450504
> pateldhaval.in.gmail.com; dhaval.iiar.res.in
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber




------------------------------

Message: 6
Date: Thu, 12 Jul 2018 17:24:11 -0400
From: Pengfei Li <ambermailpengfei.gmail.com>
Subject: Re: [AMBER] Amber16 to Amber18 upgrade?
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <399FAAAC-4FBB-4AE0-AD16-A77955F6A796.gmail.com>
Content-Type: text/plain; charset=utf-8

Hi Hirdesh,

This webpage may be helpful: http://ambermd.org/GetAmber.php#amber <http://ambermd.org/GetAmber.php#amber>.

Hope it helps,
Pengfei

> On Jul 12, 2018, at 4:46 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
>
> Hi,
>
> I have license to Amber16. Can I upgrade to Amber18 with the same license ?
>
> Thanks,
> Hirdesh
> *?*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber



------------------------------

Message: 7
Date: Thu, 12 Jul 2018 17:12:52 -0500
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] PCA multiple trajectories for mutants and wild
        type
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAAC0qOb-JSmfiUO-m=DY1zVUAzQr=MUBdr7g2Wh7We+=HiY1sw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi,

On Wed, Jul 11, 2018 at 6:48 AM Stejskal, Lenka <lenka.stejskal.15.ucl.ac.uk>
wrote:

> Dear Amber users,
>
>
> I am trying to compare multiple trajectories of either wild type and a few
> mutant of the protein to compare differences in their dynamics. I have
> several ideas how to do this and any experience/ideas would be appreciated.
>
>
> I create the matrix based on all trajectories and project the 1st and 2nd
> PC onto individual trajectories to see a difference in the occupied phase
> space. Alternatively, as I am trying to compare the mutants to the wild
> type, I could create the matrix based just on the wild type and project
> trajectories of the mutants on these eigenvectors. I believe this might be
> a better measure.


The first method you mention is fine and in fact had been used as a measure
of convergence between independent trajectories. See e.g.
https://pubs.acs.org/doi/abs/10.1021/ct400862k#/doi/abs/10.1021/ct400862k
 Or
https://pubs.acs.org/doi/abs/10.1021/jp4125099
  . Just remember if you are comparing a mutant and wildtype use only the
atoms they have in common.

>
>
> I am however making an assumption that the motion is comparable. Could
> this be an issue? Is there any way I can confirm this?
>
>
> I will also calculate the eigenvectors for each trajectory individually.
> Is there a way to compare how similar these are?


Sure - you could calculate the root mean square inner product of the
eigenvectors (cpptraj command ?modes rmsip?). See the manual for full
details

Hope this helps,

-Dan

>
>
>
> Thank you very much for your help!
>
>
> Lenka
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


------------------------------

Message: 8
Date: Thu, 12 Jul 2018 22:19:50 +0000
From: lucrecia bogado <lucre686.hotmail.com>
Subject: [AMBER] peptide bond restraints
To: "amber.ambermd.org" <amber.ambermd.org>
Message-ID:
        <DM5PR05MB3564C3790866461EA0EF37E39A590.DM5PR05MB3564.namprd05.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Amber List members,

I'm new to Amber handling and I'm trying to solve a problem:

I have been running production MD simulation of enzyme with a ligand by Amber14 with ff14sb force field in periodic water box, but amidic bond or peptide bond (CO-NH) of the ligand rotates during the dynamics

I would like to know what restrictions should be placed to avoid this rotation or where to look for such specifications, because in the user's manual they are not very clear.

I would appreciate your help.


Thank you,

Lucrecia


------------------------------

Message: 9
Date: Thu, 12 Jul 2018 15:32:58 -0700
From: Wesley Michael Botello-Smith <wmsmith.uci.edu>
Subject: Re: [AMBER] peptide bond restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAMoQph_xOXNK27rYouN0465xQ5sO9cVND+xaoFz=cqAXZfcmcw.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

If you want to restrain a dihedral rotaion, you could use nmr restraints
(nmropt=1) and write an appropriate restraint file to restrain the bond
dihedral (see section 24.1 "Distance, angle and torsional restraints" in
the amber manual).

On Thu, Jul 12, 2018 at 3:19 PM, lucrecia bogado <lucre686.hotmail.com>
wrote:

> Amber List members,
>
> I'm new to Amber handling and I'm trying to solve a problem:
>
> I have been running production MD simulation of enzyme with a ligand by
> Amber14 with ff14sb force field in periodic water box, but amidic bond or
> peptide bond (CO-NH) of the ligand rotates during the dynamics
>
> I would like to know what restrictions should be placed to avoid this
> rotation or where to look for such specifications, because in the user's
> manual they are not very clear.
>
> I would appreciate your help.
>
>
> Thank you,
>
> Lucrecia
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


------------------------------

Message: 10
Date: Thu, 12 Jul 2018 22:44:36 +0000 (UTC)
From: Kris Feher <kris.feher.yahoo.com>
Subject: [AMBER] translational diffusion coefficient from MSD
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <1251011283.3150670.1531435476974.mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear All,
I have bring up a topic that is widely discussed on the list in the past, yet I do not seem to get it right. I would like derive translational diffusion coefficient from Mean Squared Displacements. The simulations were run with iwrap =1 (see protocol below), I processed the trajectories in cpptraj with unwrap and tried to get the diffusion coefficient (second script). I was expecting that the plots the MSDs (overall, total, x,y,z) should be monotonously increasing, but this is not the case (see attached). At around 50ns there is a clear downward spike in all plots, which does not make sense. Accordingly the fitted diffusion coefficients are sort of random (certainly do not match the experimental data) and in some cases are even negative. Not using the noimage keyword does produce slightly different MSD plots with the same issues. Could anyone help me figuring out where it goes wrong?
Thanks for any idea!Kris




Production
&cntrl
imin=0, ntx=5, irest=1,
ntb=2,cut=8.0,
ntp=1, pres0=1.0,
ntc=2,
ntf=2,
ntt=3, temp0=310.0, gamma_ln=1.0,
nstlim=5000000, dt=0.002,
ioutfm=1,
iwrap=1, ioutfm=1,
ntpr=5000, ntwr=50000, ntwx=5000,
ntr=0, ig=-1,
/

- cpptraj script for trajectory processing
parm ../../dna_w.prmtop
trajin ../../5_prodNPT/dna_prod1.netcdf
trajin ../../5_prodNPT/dna_prod2.netcdf
trajin ../../5_prodNPT/dna_prod3.netcdf
trajin ../../5_prodNPT/dna_prod4.netcdf
trajin ../../5_prodNPT/dna_prod5.netcdf
trajin ../../5_prodNPT/dna_prod6.netcdf
trajin ../../5_prodNPT/dna_prod7.netcdf
trajin ../../5_prodNPT/dna_prod8.netcdf
trajin ../../5_prodNPT/dna_prod9.netcdf
trajin ../../5_prodNPT/dna_prod10.netcdf
unwrap
diffusion :1-20 separateout diffusion.dat noimage diffout DiffusionConstants.lst
-------------- next part --------------
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------------------------------

Message: 11
Date: Thu, 12 Jul 2018 19:08:22 -0400
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] peptide bond restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAGk3s-Sb7o_PDSZ-1mSaKe8PSiQKLtPnF1vELrxLvUyZmZb9dQ.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Ff14SB doesn't have ligand parameters - did you load a modified force field
for a ligand? Or is the ligand a standard peptide? If not I suspect it is
something in how the ligand was set up.

On Thu, Jul 12, 2018, 6:19 PM lucrecia bogado <lucre686.hotmail.com> wrote:

> Amber List members,
>
> I'm new to Amber handling and I'm trying to solve a problem:
>
> I have been running production MD simulation of enzyme with a ligand by
> Amber14 with ff14sb force field in periodic water box, but amidic bond or
> peptide bond (CO-NH) of the ligand rotates during the dynamics
>
> I would like to know what restrictions should be placed to avoid this
> rotation or where to look for such specifications, because in the user's
> manual they are not very clear.
>
> I would appreciate your help.
>
>
> Thank you,
>
> Lucrecia
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


------------------------------

Message: 12
Date: Fri, 13 Jul 2018 16:10:54 +0530
From: Midhun K Madhu <midhunk16.iiserb.ac.in>
Subject: [AMBER] Reduced GPU Performance
To: amber.ambermd.org
Message-ID:
        <CAFAyvOcc1is=FoPunsTxhLBKzeTZLx7FRhn8mEG0POqknSMXog.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hello all,

I was running a protein lipid system of 133,835 atom in GPU K40 using
pmemd.cuda.MPI. The speed I am getting is considerably low. I checked with
benchmark given in GPU Support, Amber website and found some issues with
the performance. Here are the speed I am getting (in ns/day):


Factor IX (90,906 atoms), NPT
-----------------------------
Given speed in K40 cards: 68.38 (4 x K40), 51.90 (2 x K40)
Speed I am getting : 33.96 (4 x K40, with 4 processors), 47.53 (2 x
K40 with 2 processors)

?Cellulose (408,609 atoms): NPT
-------------------------?-----
?
Given speed in K40 cards: 17.34 (4 x K40), 12.33 (2 x K40)
Speed I am getting : 7.86 (4 x K40, with 4 processors), 8.66 (2 x K40
with 2 processors)
?
ECC was turned off in each 4 cards and boost clocks were turned on as per
'Considerations for maximizing GPU Performance' given in the website.

The issue is - 4 cards are not giving increased speed than 2 cards! While
running my system of 133,835 atom in 4 cards and 2 cards, I am getting the
following information with nvidia-smi command:

------------------+
| 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 K40c Off | 0000:02:00.0 Off |
Off |
| 25% 52C P0 94W / 235W | 607MiB / 12287MiB | 56%
Default |
+-------------------------------+----------------------+----------------------+
| 1 Tesla K40c Off | 0000:03:00.0 Off |
Off |
| 26% 54C P0 91W / 235W | 678MiB / 12287MiB | 35%
Default |
+-------------------------------+----------------------+----------------------+
| 2 Tesla K40c Off | 0000:83:00.0 Off |
Off |
| 24% 49C P0 88W / 235W | 678MiB / 12287MiB | 31%
Default |
+-------------------------------+----------------------+----------------------+
| 3 Tesla K40c Off | 0000:84:00.0 Off |
Off |
| 25% 50C P0 90W / 235W | 679MiB / 12287MiB | 35%
Default |
+-------------------------------+----------------------+----------------------+


+-----------------------------------------------------------------------------+
| Processes: GPU
Memory |
| GPU PID Type Process name
Usage |
|=============================================================================|
| 0 21674 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
507MiB |
| 0 21675 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
| 1 21674 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
| 1 21675 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
578MiB |
| 2 21676 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
578MiB |
| 2 21677 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
| 3 21676 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
| 3 21677 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
578MiB |
+-----------------------------------------------------------------------------+




[midhun.localhost Sys3-25]$ nvidia-smi
Fri Jul 13 15:33:25 2018
+------------------------------------------------------+

| 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 K40c Off | 0000:02:00.0 Off |
Off |
| 25% 51C P0 63W / 235W | 23MiB / 12287MiB | 0%
Default |
+-------------------------------+----------------------+----------------------+
| 1 Tesla K40c Off | 0000:03:00.0 Off |
Off |
| 26% 53C P0 63W / 235W | 23MiB / 12287MiB | 0%
Default |
+-------------------------------+----------------------+----------------------+
| 2 Tesla K40c Off | 0000:83:00.0 Off |
Off |
| 32% 71C P0 145W / 235W | 677MiB / 12287MiB | 88%
Default |
+-------------------------------+----------------------+----------------------+
| 3 Tesla K40c Off | 0000:84:00.0 Off |
Off |
| 32% 71C P0 144W / 235W | 763MiB / 12287MiB | 99%
Default |
+-------------------------------+----------------------+----------------------+


+-----------------------------------------------------------------------------+
| Processes: GPU
Memory |
| GPU PID Type Process name
Usage |
|=============================================================================|
| 2 21795 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
576MiB |
| 2 21796 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
| 3 21795 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
| 3 21796 C ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
663MiB |
+-----------------------------------------------------------------------------+


?Why the GPU usage is like 56%,35%,31% and 35% while running in 4 GPU cards
while running in 2 cards gives 88% and 99%?

I was getting 27.11 ns/day in 2xK40 and 21.09 ns/day in 4xK40 cards. Why am
I not getting an increased speed? Please reply.

--
*MIDHUN K MADHU*
Ph.D Student
Dept. of Biological Sciences
IISER Bhopal
--------------------------------
------------------------------
Message: 13
Date: Fri, 13 Jul 2018 12:48:15 +0200
From: Chetna Tyagi <cheta231.gmail.com>
Subject: [AMBER] Fwd: issues with accelerated MD in chloroform
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAJ4urR4tBi0RmaTwPgnocnstarG8z=BTw4hLCOq6tDOYg0tkMg.mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Amber users,
While carrying out an aMD simulation in chloroform solvent of my peptide,
only dihedral boost is applied even after iamd=3 (dual boost option).
The Ethresh value when lower, the calculation goes without any error except
that the boost energy is 0 kcal/mol at every step.
When the Ethresh value is higher than the average potential energy (as it
should be), the calculation proceeds but the output amd.log file looks like
this.
[image: image.png]
Can anyone explain what's wrong here? Ideally, for the boost to be applied
to the system, potential energy should be below the specified criterion, in
this case the Ethresh. Why should it show errors?
Any help would be appreciated.
--
Best wishes
Chetna
-------------- next part --------------
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------------------------------
Message: 14
Date: Fri, 13 Jul 2018 08:44:15 -0300 (UYT)
From: Matias Machado <mmachado.pasteur.edu.uy>
Subject: Re: [AMBER] Reduced GPU Performance
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <4acaed4b-4cc0-4e44-a9c2-8bc6125943df.free.ipmont.lan>
Content-Type: text/plain; charset=utf-8
Dear Midhun,
It seems all your graphic cards are in the same machine, so I would try pmemd.cuda instead of pmemd.cuda.MPI (this command is optimized to run through nodes)
Best,
Mat?as
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[http://pasteur.uy/en/laboratorios-eng/lsbm]
[http://www.sirahff.com]
----- Mensaje original -----
De: "Midhun K Madhu" <midhunk16.iiserb.ac.in>
Para: amber.ambermd.org
Enviados: Viernes, 13 de Julio 2018 7:40:54
Asunto: [AMBER] Reduced GPU Performance
Hello all,
I was running a protein lipid system of 133,835 atom in GPU K40 using
pmemd.cuda.MPI. The speed I am getting is considerably low. I checked with
benchmark given in GPU Support, Amber website and found some issues with
the performance. Here are the speed I am getting (in ns/day):
Factor IX (90,906 atoms), NPT
-----------------------------
Given speed in K40 cards: 68.38 (4 x K40), 51.90 (2 x K40)
Speed I am getting      : 33.96 (4 x K40, with 4 processors), 47.53 (2 x
K40 with 2 processors)
?Cellulose (408,609 atoms): NPT
-------------------------?-----
?
Given speed in K40 cards: 17.34 (4 x K40), 12.33 (2 x K40)
Speed I am getting      : 7.86  (4 x K40, with 4 processors), 8.66 (2 x K40
with 2 processors)
?
ECC was turned off in each 4 cards and boost clocks were turned on as per
'Considerations for maximizing GPU Performance' given in the website.
The issue is - 4 cards are not giving increased speed than 2 cards! While
running my system of 133,835 atom in 4 cards and 2 cards, I am getting the
following information with nvidia-smi command:
------------------+
| 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 K40c          Off  | 0000:02:00.0     Off |
Off |
| 25%   52C    P0    94W / 235W |    607MiB / 12287MiB |     56%
Default |
+-------------------------------+----------------------+----------------------+
|   1  Tesla K40c          Off  | 0000:03:00.0     Off |
Off |
| 26%   54C    P0    91W / 235W |    678MiB / 12287MiB |     35%
Default |
+-------------------------------+----------------------+----------------------+
|   2  Tesla K40c          Off  | 0000:83:00.0     Off |
Off |
| 24%   49C    P0    88W / 235W |    678MiB / 12287MiB |     31%
Default |
+-------------------------------+----------------------+----------------------+
|   3  Tesla K40c          Off  | 0000:84:00.0     Off |
Off |
| 25%   50C    P0    90W / 235W |    679MiB / 12287MiB |     35%
Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU
Memory |
|  GPU       PID  Type  Process name
Usage      |
|=============================================================================|
|    0     21674    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
507MiB |
|    0     21675    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
|    1     21674    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
|    1     21675    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
578MiB |
|    2     21676    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
578MiB |
|    2     21677    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
|    3     21676    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
|    3     21677    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
578MiB |
+-----------------------------------------------------------------------------+
[midhun.localhost Sys3-25]$ nvidia-smi
Fri Jul 13 15:33:25 2018
+------------------------------------------------------+
| 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 K40c          Off  | 0000:02:00.0     Off |
Off |
| 25%   51C    P0    63W / 235W |     23MiB / 12287MiB |      0%
Default |
+-------------------------------+----------------------+----------------------+
|   1  Tesla K40c          Off  | 0000:03:00.0     Off |
Off |
| 26%   53C    P0    63W / 235W |     23MiB / 12287MiB |      0%
Default |
+-------------------------------+----------------------+----------------------+
|   2  Tesla K40c          Off  | 0000:83:00.0     Off |
Off |
| 32%   71C    P0   145W / 235W |    677MiB / 12287MiB |     88%
Default |
+-------------------------------+----------------------+----------------------+
|   3  Tesla K40c          Off  | 0000:84:00.0     Off |
Off |
| 32%   71C    P0   144W / 235W |    763MiB / 12287MiB |     99%
Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU
Memory |
|  GPU       PID  Type  Process name
Usage      |
|=============================================================================|
|    2     21795    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
576MiB |
|    2     21796    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
|    3     21795    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
73MiB |
|    3     21796    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
663MiB |
+-----------------------------------------------------------------------------+
?Why the GPU usage is like 56%,35%,31% and 35% while running in 4 GPU cards
while running in 2 cards gives 88% and 99%?
I was getting 27.11 ns/day in 2xK40 and 21.09 ns/day in 4xK40 cards. Why am
I not getting an increased speed? Please reply.
--
*MIDHUN K MADHU*
Ph.D Student
Dept. of Biological Sciences
IISER Bhopal
--------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 15
Date: Fri, 13 Jul 2018 15:12:50 +0200
From: Raimon Fabregat <raimon.fabregat.epfl.ch>
Subject: [AMBER] Single Point Calculation on trajectory
To: AMBER.ambermd.org
Message-ID: <c98bf56c-8d1b-308a-8a61-fe1f0d2eee90.epfl.ch>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear all,
I am trying to perform a Single Point Calculation (SPC) (to compute the
potential energy) of a series of molecular configurations stored in a
trajectory file.
To do that I am doing a geometry optimization with 0 steps in each
structure, but I am not sure it is working. The input file I am using is:
spc.mdin:
     ?&cntrl
     ?? imin?? = 5,
     ?? maxcyc = 0,
     ?? cut = 999.0, ??? ! The system is just an isolated molecule
     ?? rgbmax = 999.0,
     ?? ifqnt = 1
     ?? ntb=0
     ?/
     ?&qmmm
     ?? qmcut = 9999.9,
     ?? qmmask = '.*',
     ?? qmcharge = 0,
     ?? qm_theory = PM6-DH+,
     ?? qmshake = 1,
     ?/
     ?&wt type='END'
     ?/
To check that this is indeed doing what I want, I applied it to a
trajectory generated with the same potential energy function, using the
following input file:
remd.mdin.001:
 ?&cntrl
 ?? ntx=1,
 ?? nstlim=200, dt=0.001,
 ?? numexchg=20000,
 ?? irest=0, ntt=3, gamma_ln=1.0,
 ?? temp0=300, ig=963,
 ?? ntc=2, ntf=2, nscm=100,
 ?? ntb=0, igb=0,
 ?? cut=999.0, rgbmax=999.0,
 ?? ntpr=100, ntwx=100, ntwr=10000,
 ?? ioutfm=1,
 ?? ntc=2
 ?? ifqnt=1
 ?/
 ?&qmmm
 ?? qmcut = 9999.9,
 ?? qmmask = '.*',
 ?? qmcharge = 0,
 ?? qm_theory = PM6-DH+,
 ?? dftb_disper = 0,
 ?? qmshake = 1,
 ?/
 ?&wt type='END'
 ?/
Which as I mentioned it has the same potential energy function. However,
the energies printed from the trajectory don't quite match the ones
computed using the SPC.
This is the remd.mdout.001 file were I get the energies from the simulation
 ? ?? 4.? RESULTS
--------------------------------------------------------------------------------
 ?NSTEP =??????? 0?? TIME(PS) =?????? 0.000? TEMP(K) =???? 0.00 PRESS
=???? 0.0
 ?Etot?? =??????? 55.8629? EKtot?? =???????? 0.0000? EPtot =??????? 55.8629
 ?BOND?? =???????? 0.0000? ANGLE?? =???????? 0.0000? DIHED =???????? 0.0000
 ?1-4 NB =???????? 0.0000? 1-4 EEL =???????? 0.0000? VDWAALS =????????
0.0000
 ?EELEC? =???????? 0.0000? EHBOND? =???????? 0.0000? RESTRAINT =????????
0.0000
 ?PM6ESCF=??????? 55.8629
 ?TEMP0? =?????? 300.0000? REPNUM? =????????????? 1? EXCHANGE#
=????????????? 0
 ?------------------------------------------------------------------------------
 ?NMR restraints: Bond =??? 0.000?? Angle =???? 0.000?? Torsion =???? 0.000
===============================================================================
| RE_POSITION Moving by?? 0.041055? 0.028284 -0.019654
NetCDF error: NetCDF: Variable not found
 ? at write replica mytargettemp
 ?NSTEP =????? 100?? TIME(PS) =?????? 0.100? TEMP(K) =??? 55.15 PRESS
=???? 0.0
 ?Etot?? =??????? 60.8920? EKtot?? =???????? 5.5893? EPtot =??????? 55.3027
 ?BOND?? =???????? 0.0000? ANGLE?? =???????? 0.0000? DIHED =???????? 0.0000
 ?1-4 NB =???????? 0.0000? 1-4 EEL =???????? 0.0000? VDWAALS =????????
0.0000
 ?EELEC? =???????? 0.0000? EHBOND? =???????? 0.0000? RESTRAINT =????????
0.0000
 ?PM6ESCF=??????? 55.3027
 ?TEMP0? =?????? 300.0000? REPNUM? =????????????? 1? EXCHANGE#
=????????????? 1
 ?------------------------------------------------------------------------------
 ?NMR restraints: Bond =??? 0.000?? Angle =???? 0.000?? Torsion =???? 0.000
===============================================================================
| RE_POSITION Moving by? -0.035491 -0.048501? 0.026206
NetCDF error: NetCDF: Variable not found
 ? at write replica mytargettemp
 ?NSTEP =????? 200?? TIME(PS) =?????? 0.200? TEMP(K) =??? 87.63 PRESS
=???? 0.0
 ?Etot?? =??????? 65.2281? EKtot?? =???????? 8.8813? EPtot =??????? 56.3467
 ?BOND?? =???????? 0.0000? ANGLE?? =???????? 0.0000? DIHED =???????? 0.0000
 ?1-4 NB =???????? 0.0000? 1-4 EEL =???????? 0.0000? VDWAALS =????????
0.0000
 ?EELEC? =???????? 0.0000? EHBOND? =???????? 0.0000? RESTRAINT =????????
0.0000
 ?PM6ESCF=??????? 56.3467
 ?TEMP0? =?????? 300.0000? REPNUM? =????????????? 1? EXCHANGE#
=????????????? 1
 ?------------------------------------------------------------------------------
 ?NMR restraints: Bond =??? 0.000?? Angle =???? 0.000?? Torsion =???? 0.000
===============================================================================
| RE_POSITION Moving by?? 0.021387 -0.059176? 0.025757
NetCDF error: NetCDF: Variable not found
 ? at write replica mytargettemp
 ?NSTEP =????? 300?? TIME(PS) =?????? 0.300? TEMP(K) =?? 105.27 PRESS
=???? 0.0
 ?Etot?? =??????? 70.0486? EKtot?? =??????? 10.6692? EPtot =??????? 59.3794
 ?BOND?? =???????? 0.0000? ANGLE?? =???????? 0.0000? DIHED =???????? 0.0000
 ?1-4 NB =???????? 0.0000? 1-4 EEL =???????? 0.0000? VDWAALS =????????
0.0000
 ?EELEC? =???????? 0.0000? EHBOND? =???????? 0.0000? RESTRAINT =????????
0.0000
 ?PM6ESCF=??????? 59.3794
 ?TEMP0? =?????? 300.0000? REPNUM? =????????????? 1? EXCHANGE#
=????????????? 2
 ?------------------------------------------------------------------------------
And this is the output from the SPC in the same first 3 structures from
the trajectory (corresponding to the previous output):
 ? 4.? RESULTS
--------------------------------------------------------------------------------
 ? Maximum number of minimization cycles reached.
 ??????????????????? FINAL RESULTS
 ?? NSTEP?????? ENERGY????????? RMS??????????? GMAX NAME??? NUMBER
 ????? 1?????? 5.5525E+01???? 7.3313E+00???? 1.9797E+01 C7???????? 14
 ?BOND??? =??????? 0.0000? ANGLE?? =??????? 0.0000? DIHED =??????? 0.0000
 ?VDWAALS =??????? 0.0000? EEL???? =??????? 0.0000? HBOND =??????? 0.0000
 ?1-4 VDW =??????? 0.0000? 1-4 EEL =??????? 0.0000? RESTRAINT =???????
0.0000
 ?PM6ESCF =?????? 55.5251
minimization completed, ENE= 0.55525091E+02 RMS= 0.733131E+01
minimizing coord set #???? 2
 ? Maximum number of minimization cycles reached.
 ??????????????????? FINAL RESULTS
 ?? NSTEP?????? ENERGY????????? RMS??????????? GMAX NAME??? NUMBER
 ????? 1?????? 5.6441E+01???? 7.4006E+00???? 2.0826E+01 C11??????? 28
 ?BOND??? =??????? 0.0000? ANGLE?? =??????? 0.0000? DIHED =??????? 0.0000
 ?VDWAALS =??????? 0.0000? EEL???? =??????? 0.0000? HBOND =??????? 0.0000
 ?1-4 VDW =??????? 0.0000? 1-4 EEL =??????? 0.0000? RESTRAINT =???????
0.0000
 ?PM6ESCF =?????? 56.4414
minimization completed, ENE= 0.56441442E+02 RMS= 0.740056E+01
minimizing coord set #???? 3
 ? Maximum number of minimization cycles reached.
 ??????????????????? FINAL RESULTS
 ?? NSTEP?????? ENERGY????????? RMS??????????? GMAX NAME??? NUMBER
 ????? 1?????? 5.9277E+01???? 9.9923E+00???? 4.2688E+01 C3????????? 4
 ?BOND??? =??????? 0.0000? ANGLE?? =??????? 0.0000? DIHED =??????? 0.0000
 ?VDWAALS =??????? 0.0000? EEL???? =??????? 0.0000? HBOND =??????? 0.0000
 ?1-4 VDW =??????? 0.0000? 1-4 EEL =??????? 0.0000? RESTRAINT =???????
0.0000
 ?PM6ESCF =?????? 59.2766
minimization completed, ENE= 0.59276627E+02 RMS= 0.999230E+01
minimizing coord set #???? 4
 ? Maximum number of minimization cycles reached.
The energies then are:
 From simulation??? ??? ??? From SPC
55.5251?????????? 55.3027
56.4414?????????? 56.3467
59.2766?????????? 59.3794
63.4846?????????? 63.6437
63.5524?????????? 63.3793
63.1787?????????? 62.8946
65.2079?????????? 65.0181
74.7678?????????? 74.1447
67.0064?????????? 68.0420
70.3709?????????? 70.7692
They are very correlated, but still different. Does anybody know what is
going on???
Thanks a lot for your help, I deeply appreciate it!!
All the best,
Raimon
------------------------------
Message: 16
Date: Fri, 13 Jul 2018 21:51:05 +0500
From: Syeda <computationalchemist84.gmail.com>
Subject: [AMBER] Per-residue energy decomposition by MMPBSA.pl
To: amber.ambermd.org
Message-ID:
        <CAEhJutAYQFb8hWtHsVJOY=PfNL4Q1sUy_6oAFgXfbgWCuyPt8A.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Hi,
I am trying to perform per residue binding energy decomposition on a
protein-ligand complex by using Amber MMPBSA.pl script to find out the
differences in energies of each residue in both apo and holo systems.
The generated output is a large file containing the following information:
    Number    Residue       SINT                  BINT
TINT                  SVDW                  BVDW                  TVDW
SELE                  BELE                  TELE
SGAS                  BGAS                  TGAS                   SGB
BGB                   TGB                SGBSUR
BGBSUR              TGBSUR                SGBSOL
BGBSOL                TGBSOL                SGBTOT
BGBTOT                TGBTOT
It is difficult to understand the output of "snapshot_statistics.out" file.
There is an option in mmpbsa.py to add dec_verbose to the input file in
order to reduce/increase the details in the out file as follows:
dec_verbose:
Set the level of output to print in the decomp_output file.
0: DELTA energy, total contribution only.
1: DELTA energy, total, sidechain, and backbone contributions.
2: Complex, Receptor, Ligand, and DELTA energies, total contribution only.
3: Complex,Receptor, Ligand, and DELTA energies, total, sidechain, and
backbone contributions (all data) (Default 0)
Is there any way to add verbose in perl script to get the Complex,
Receptor, Ligand, and DELTA energies, for total contribution only?
Secondly, can these results be interpreted as plots of binding energies
versus residues?
Any information you can provide me would be greatly appreciated.
Many Thanks
Following is the input file:
Sample mm_pbsa.in3 file for MM/GBSA decomposotion. #
# Input parameters for mm_pbsa.pl
# This example just generates snapshots from a trajectory file
#
# Holger Gohlke
# 08.01.2002
#
################################################################################
.GENERAL
#
# General parameters
#   0: means NO; >0: means YES
#
#   mm_pbsa allows to calculate (absolute) free energies for one molecular
#     species or a free energy difference according to:
#
#     Receptor + Ligand = Complex,
#     DeltaG = G(Complex) - G(Receptor) - G(Ligand).
#
#   PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added during
#            generation of snapshots as well as during mm_pbsa calculations.
#   PATH - Specifies the location where to store or get snapshots.
#
#   COMPLEX - Set to 1 if free energy difference is calculated.
#   RECEPTOR - Set to 1 if either (absolute) free energy or free energy
#              difference are calculated.
#   LIGAND - Set to 1 if free energy difference is calculated.
#
#   COMPT - parmtop file for the complex (not necessary for option GC).
#   RECPT - parmtop file for the receptor (not necessary for option GC).
#   LIGPT - parmtop file for the ligand (not necessary for option GC).
#
#   GC - Snapshots are generated from trajectories (see below).
#   AS - Residues are mutated during generation of snapshots from
trajectories.
#   DC - Decompose the free energies into individual contributions
#        (only works with MM and GB).
#
#   MM - Calculation of gas phase energies using sander.
#   GB - Calculation of desolvation free energies using the GB models in
sander
#        (see below).
#   PB - Calculation of desolvation free energies using delphi (see below).
#   MS - Calculation of nonpolar contributions to desolvation using molsurf
#        (see below).
#        If MS == 0, nonpolar contributions are calculated with the LCPO
method
#        in sander.
#   NM - Calculation of entropies with nmode.
#
PREFIX                btn1
PATH                  ./
#
COMPLEX               1
RECEPTOR              1
LIGAND                1
#
COMPT                 compl.prmtop
RECPT                 prot.prmtop
LIGPT                 lig.prmtop
#
GC                    0
AS                    0
DC                    1
#
MM                    1
GB                    1
PB                    0
MS                    0
#
NM                    0
#
#
################################################################################
.MM
#
# MM parameters (this section is only relevant if MM = 1 above)
#
#   The following parameters are passed to sander.
#   For further details see the sander documentation.
#
#   DIELC - Dielectricity constant for electrostatic interactions.
#           Note: This is not related to GB calculations.
#
DIELC                 1.0
#
################################################################################
.GB
#
# GB parameters (this section is only relevant if GB = 1 above)
#
#   The first group of the following parameters are passed to sander.
#   For further details see the sander documentation.
#
#   IGB - Switches between Tsui's GB (1), Onufriev's GB (2, 5).
#   GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc.
#          Decomposition only works with ICOSA.
#   SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.
#   EXTDIEL - Dielectricity constant for the solvent.
#   INTDIEL - Dielectricity constant for the solute
#
#   SURFTEN / SURFOFF - Values used to compute the nonpolar contribution
Gnp to
#                   the desolvation according to Gnp = SURFTEN * SASA +
SURFOFF.
#
IGB                   2
GBSA                  2
SALTCON               0.00
EXTDIEL               80.0
INTDIEL               1.0
#
SURFTEN               0.00542
SURFOFF               0.92
#
################################################################################
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
#   PROBE - Radius of the probe sphere used to calculate the SAS.
#           Since Bondi radii are already augmented by 1.4A, PROBE should
be 0.0
#
PROBE                 0.0
#
#
################################################################################
.DECOMP
#
# Energy decomposition parameters (this section is only relevant if DC = 1
above)
#
#   Energy decomposition is performed for gasphase energies, desolvation
free
#     energies calculated with GB, and nonpolar contributions to desolvation
#     using the LCPO method.
#   For amino acids, decomposition is also performed with respect to
backbone
#     and sidechain atoms.
#
#   DCTYPE - Values of 1 or 2 yield a decomposition on a per-residue basis,
#            values of 3 or 4 yield a decomposition on a pairwise
per-residue
#               basis. For the latter, so far the number of pairs must not
#               exceed the number of residues in the molecule considered.
#            Values 1 or 3 add 1-4 interactions to bond contributions.
#            Values 2 or 4 add 1-4 interactions to either electrostatic or
vdW
#              contributions.
#
#   COMREC - Residues belonging to the receptor molecule IN THE COMPLEX.
#   COMLIG - Residues belonging to the ligand molecule IN THE COMPLEX.
#   RECRES - Residues in the receptor molecule.
#   LIGRES - Residues in the ligand molecule.
#   {COM,REC,LIG}PRI - Residues considered for output.
#   {REC,LIG}MAP - Residues in the complex which are equivalent to the
residues
#                  in the receptor molecule or the ligand molecule.
#
DCTYPE                2
#
COMREC                1-497
COMLIG                498-498
COMPRI                1-498
RECRES                1-497
RECPRI                1-497
RECMAP                1-497
LIGRES                1-1
LIGPRI                1-1
LIGMAP                498-498
#
#
################################################################################
------------------------------
Message: 17
Date: Fri, 13 Jul 2018 23:01:00 +0530
From: Chhaya Singh <chhayasingh014.gmail.com>
Subject: [AMBER] convert trajectories files in AMBER
To: AMBER Mailing List <amber.ambermd.org>, david.case.rutgers.edu,
        Carlos Simmerling <carlos.simmerling.gmail.com>
Message-ID:
        <CANHFQqARgxqWgJJTzhuN2J3OS3=wO=MMktTmZzQHCL7RJ6Zm1w.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
I have a file md.out which basically saves all the information after every
0.1ps but I want to generate a file having information at an interval of
1ps or 10 ps .is there any way to save every 10th or 100th frame using
cpptraj?
my trajectories is in NetCDF(.nc) format.
I want to do this because when I load this files in vmd it takes a lot of
time. so I want short time duration so that I can load my files fastly.
is there a way to do all this without running any new simulations.
------------------------------
Message: 18
Date: Fri, 13 Jul 2018 19:43:34 +0200
From: Charles-Alexandre Mattelaer <camattelaer01.gmail.com>
Subject: Re: [AMBER] convert trajectories files in AMBER
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAB=oofU-+Xj3Q-7pQqfcG1pgHMk1iy=uGsOPXJ+iOU_CcfNv3Q.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear Chhaya
Check the cpptraj manual. You can use trajin for this following the syntax
Trajin yourtrajectory.nc start stop offset
Trajout yourshortertrajectory.nc
Run
Set the offset to a value of 10 or 100 or whatever you think is appropriate
and the trajout will write every 10th or 100th frame to a new trajectory.
Btw usually the ".out" is the file containing energy info etc and not the
trajectory.
Kind regards
Charles-Alexandre Mattelaer
Op vr 13 jul. 2018 19:38 schreef Chhaya Singh <chhayasingh014.gmail.com>:
> I have a file md.out which basically saves all the information after every
> 0.1ps but I want to generate a file having information at an interval of
> 1ps or 10 ps .is there any way to save every 10th or 100th frame using
> cpptraj?
>
> my trajectories is in NetCDF(.nc) format.
>
> I want to do this because when I load this files in vmd it takes a lot of
> time. so I want short time duration so that I can load my files fastly.
> is there a way to do all this without running any new simulations.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 19
Date: Fri, 13 Jul 2018 18:23:26 +0000
From: lucrecia bogado <lucre686.hotmail.com>
Subject: Re: [AMBER] peptide bond restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <DM5PR05MB3564CD0A6F84CFFF421E65109A580.DM5PR05MB3564.namprd05.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
for the ligand I have used the force field GAFF, with RESP charges.
thanks
________________________________
De: Carlos Simmerling <carlos.simmerling.gmail.com>
Enviado: jueves, 12 de julio de 2018 20:08:22
Para: AMBER Mailing List
Asunto: Re: [AMBER] peptide bond restraints
Ff14SB doesn't have ligand parameters - did you load a modified force field
for a ligand? Or is the ligand a standard peptide? If not I suspect it is
something in how the ligand was set up.
On Thu, Jul 12, 2018, 6:19 PM lucrecia bogado <lucre686.hotmail.com> wrote:
> Amber List members,
>
> I'm new to Amber handling and I'm trying to solve a problem:
>
> I have been running production MD simulation of enzyme with a ligand by
> Amber14 with ff14sb force field in periodic  water box, but amidic bond or
> peptide bond (CO-NH) of the ligand rotates during the dynamics
>
> I would like to know what restrictions should be placed to avoid this
> rotation or where to look for such specifications, because in the user's
> manual they are not very clear.
>
> I would appreciate your help.
>
>
> Thank you,
>
> Lucrecia
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
Message: 20
Date: Fri, 13 Jul 2018 14:30:54 -0400
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] peptide bond restraints
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <CAGk3s-Tb+gcS4XSfgim1x5JoBPwr51w+mmV+-4a7b6kQHYmGdA.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
It sounds like maybe something isn't right about the gaff setup for your
ligand. It might help to post a question about applying gaff to your
ligand, explaining the functional groups and what happens. I think it's
very unlikely that this is related to ff14SB.
On Fri, Jul 13, 2018, 2:23 PM lucrecia bogado <lucre686.hotmail.com> wrote:
> for the ligand I have used the force field GAFF, with RESP charges.
>
> thanks
>
> ________________________________
> De: Carlos Simmerling <carlos.simmerling.gmail.com>
> Enviado: jueves, 12 de julio de 2018 20:08:22
> Para: AMBER Mailing List
> Asunto: Re: [AMBER] peptide bond restraints
>
> Ff14SB doesn't have ligand parameters - did you load a modified force field
> for a ligand? Or is the ligand a standard peptide? If not I suspect it is
> something in how the ligand was set up.
>
> On Thu, Jul 12, 2018, 6:19 PM lucrecia bogado <lucre686.hotmail.com>
> wrote:
>
> > Amber List members,
> >
> > I'm new to Amber handling and I'm trying to solve a problem:
> >
> > I have been running production MD simulation of enzyme with a ligand by
> > Amber14 with ff14sb force field in periodic  water box, but amidic bond
> or
> > peptide bond (CO-NH) of the ligand rotates during the dynamics
> >
> > I would like to know what restrictions should be placed to avoid this
> > rotation or where to look for such specifications, because in the user's
> > manual they are not very clear.
> >
> > I would appreciate your help.
> >
> >
> > Thank you,
> >
> > Lucrecia
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
------------------------------
Message: 21
Date: Fri, 13 Jul 2018 14:45:47 -0400
From: Ross Walker <ross.rosswalker.co.uk>
Subject: Re: [AMBER] Reduced GPU Performance
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <05D7B235-6ACB-43A6-AAE3-FEAE0DA74DF0.rosswalker.co.uk>
Content-Type: text/plain;       charset=utf-8
Hi Midhun,
Please read the following page in it's entirety: http://ambermd.org/gpus/ <http://ambermd.org/gpus/>  - It has a lot of information about how to run most efficiently. It is not surprising that you do not see scaling over 4 GPUs. You need special hardware to do it and even then the scaling is poor. The recommended approach is to run single GPU jobs with pmemd.cuda and just run 4 individual calculations each one on a different GPU. The webpage explains how to do this.
All the best
Ross
> On Jul 13, 2018, at 06:40, Midhun K Madhu <midhunk16.iiserb.ac.in> wrote:
>
> Hello all,
>
> I was running a protein lipid system of 133,835 atom in GPU K40 using
> pmemd.cuda.MPI. The speed I am getting is considerably low. I checked with
> benchmark given in GPU Support, Amber website and found some issues with
> the performance. Here are the speed I am getting (in ns/day):
>
>
> Factor IX (90,906 atoms), NPT
> -----------------------------
> Given speed in K40 cards: 68.38 (4 x K40), 51.90 (2 x K40)
> Speed I am getting      : 33.96 (4 x K40, with 4 processors), 47.53 (2 x
> K40 with 2 processors)
>
> ?Cellulose (408,609 atoms): NPT
> -------------------------?-----
> ?
> Given speed in K40 cards: 17.34 (4 x K40), 12.33 (2 x K40)
> Speed I am getting      : 7.86  (4 x K40, with 4 processors), 8.66 (2 x K40
> with 2 processors)
> ?
> ECC was turned off in each 4 cards and boost clocks were turned on as per
> 'Considerations for maximizing GPU Performance' given in the website.
>
> The issue is - 4 cards are not giving increased speed than 2 cards! While
> running my system of 133,835 atom in 4 cards and 2 cards, I am getting the
> following information with nvidia-smi command:
>
> ------------------+
> | 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 K40c          Off  | 0000:02:00.0     Off |
> Off |
> | 25%   52C    P0    94W / 235W |    607MiB / 12287MiB |     56%
> Default |
> +-------------------------------+----------------------+----------------------+
> |   1  Tesla K40c          Off  | 0000:03:00.0     Off |
> Off |
> | 26%   54C    P0    91W / 235W |    678MiB / 12287MiB |     35%
> Default |
> +-------------------------------+----------------------+----------------------+
> |   2  Tesla K40c          Off  | 0000:83:00.0     Off |
> Off |
> | 24%   49C    P0    88W / 235W |    678MiB / 12287MiB |     31%
> Default |
> +-------------------------------+----------------------+----------------------+
> |   3  Tesla K40c          Off  | 0000:84:00.0     Off |
> Off |
> | 25%   50C    P0    90W / 235W |    679MiB / 12287MiB |     35%
> Default |
> +-------------------------------+----------------------+----------------------+
>
>
> +-----------------------------------------------------------------------------+
> | Processes:                                                       GPU
> Memory |
> |  GPU       PID  Type  Process name
> Usage      |
> |=============================================================================|
> |    0     21674    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 507MiB |
> |    0     21675    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 73MiB |
> |    1     21674    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 73MiB |
> |    1     21675    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 578MiB |
> |    2     21676    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 578MiB |
> |    2     21677    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 73MiB |
> |    3     21676    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 73MiB |
> |    3     21677    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 578MiB |
> +-----------------------------------------------------------------------------+
>
>
>
>
> [midhun.localhost Sys3-25]$ nvidia-smi
> Fri Jul 13 15:33:25 2018
> +------------------------------------------------------+
>
> | 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 K40c          Off  | 0000:02:00.0     Off |
> Off |
> | 25%   51C    P0    63W / 235W |     23MiB / 12287MiB |      0%
> Default |
> +-------------------------------+----------------------+----------------------+
> |   1  Tesla K40c          Off  | 0000:03:00.0     Off |
> Off |
> | 26%   53C    P0    63W / 235W |     23MiB / 12287MiB |      0%
> Default |
> +-------------------------------+----------------------+----------------------+
> |   2  Tesla K40c          Off  | 0000:83:00.0     Off |
> Off |
> | 32%   71C    P0   145W / 235W |    677MiB / 12287MiB |     88%
> Default |
> +-------------------------------+----------------------+----------------------+
> |   3  Tesla K40c          Off  | 0000:84:00.0     Off |
> Off |
> | 32%   71C    P0   144W / 235W |    763MiB / 12287MiB |     99%
> Default |
> +-------------------------------+----------------------+----------------------+
>
>
> +-----------------------------------------------------------------------------+
> | Processes:                                                       GPU
> Memory |
> |  GPU       PID  Type  Process name
> Usage      |
> |=============================================================================|
> |    2     21795    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 576MiB |
> |    2     21796    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 73MiB |
> |    3     21795    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 73MiB |
> |    3     21796    C   ...midhun/AMBER16/amber16/bin/pmemd.cuda.MPI
> 663MiB |
> +-----------------------------------------------------------------------------+
>
>
> ?Why the GPU usage is like 56%,35%,31% and 35% while running in 4 GPU cards
> while running in 2 cards gives 88% and 99%?
>
> I was getting 27.11 ns/day in 2xK40 and 21.09 ns/day in 4xK40 cards. Why am
> I not getting an increased speed? Please reply.
>
>
>
> --
>
> *MIDHUN K MADHU*
> Ph.D Student
> Dept. of Biological Sciences
> IISER Bhopal
> --------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
------------------------------
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End of AMBER Digest, Vol 2349, Issue 1
**************************************
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Received on Tue Jul 17 2018 - 08:00:03 PDT