[gmx-users] gromacs.org_gmx-users Digest, Vol 185, Issue 55

ABEL Stephane Stephane.ABEL at cea.fr
Tue Sep 17 12:10:59 CEST 2019


Did you try to compute the msd for only few atoms (for instance phosphorus), the COM of each lipid or use different segments of your trajectory ? This approach is sometime used. 



Message: 2
Date: Tue, 17 Sep 2019 08:46:38 +0200
From: Martin Kern <martin.kern at uni-konstanz.de>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] RAM usage of gmx msd
Message-ID: <75551d1f-9cdf-ea8d-ac2d-6576b548d735 at uni-konstanz.de>
Content-Type: text/plain; charset=utf-8; format=flowed

Hello everyone.

I simulated a cell membrane and would like to calculate lateral
diffusion of lipids. I tried this using the gmx msd command.
Unfortunately this uses enormous amounts of RAM. The process runs
without error until it is killed by the operating system. No output file
is created at that time.

The membrane contains around 400 lipids and I simulated for 1100ns which
is 220000 frames. The total size of the xtc file is around 150 GB. I use
GROMACS 2016.4 with GPU support. The command I used was:
gmx msd -s mdrun.tpr -f mdrun.xtc -n key_atoms.ndx -lateral z -o

I found an old email that also mentions the high RAM usage of gmx msd
but it didn't get a reply.

I also tried reducing the RAM usage by creating a trajectory that only
includes the key atoms. This attempt resulted in a segmentation fault.
Here is what I tried:
gmx trjconv -f mdrun.xtc -n key_atoms.ndx -o mdrun_key_atoms.xtc
gmx convert-tpr -f mdrun.tpr -n key_atoms.ndx -o mdrun_key_atoms.tpr
gmx msd -s mdrun_key_atoms.tpr -f mdrun_key_atoms.xtc -n key_atoms.ndx
-lateral z -o lateraal_diffusion.xvg

I'm grateful for any suggestion.

Best regards
Martin Kern


Message: 3
Date: Tue, 17 Sep 2019 14:43:28 +0530
From: Navneet Kumar Singh <navneetcdl at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Equilibration Problem.
        <CAOvdM4UffTrCgF=vw_i=QmD7Fdgok9BHF5sBRJP1teAR4xGZNg at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hello Everyone!

Trying to simulate a system build in PACKMOL having peptides, water and
small molecules. Energy minimization and other process for setting up md
simulation went fine.

NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
Average required temperature maintained.

*Energy                      Average   Err.Est.     RMSD
                  0.261272     0.49      49.1061        1.55678  (bar)*

*Density                            213.361       0.58       1.18799
       4.08348 (kg/m^3)*

*Temperature                       300.002       0.04      2.38265
-0.0854606  (K)*


*Temperature 300k is fine. But the density of the system is 213.361 and
attached graph (https://fil.email/ic2yZ4x3 <https://fil.email/ic2yZ4x3>)
shows unstable system. I extended it to 10 ns but still follows same
pattern. What can be the problem with this? Using TIP3P water model with
CHARMM36 force field to simulate the system.*

     Thanks & Regards

[image: photo]

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>

<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

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