[gmx-users] Truncated .trr file size - 20% smaller than expected

Douglas Grahame dgrahame at uoguelph.ca
Fri May 9 19:46:41 CEST 2014

Hi there this is my first time posting here so my apologies if I disregard
any general formatting rules! In any event on to my question/problem.


I am fairly new to MD simulations with much more background on the
biological side than the simulation side. That being said, I have been
receiving training from another member in the lab and have just started my
simulations of a 325 residue protein using GROMACS 4.5.5. My issue has come
from the fact that when I grompp my EM.mdp, NVT.mdp, or MPT.mdp files
everything seems to be fine ie. No errors or issues and the file sizes match
the expected output size. However, when I run my simulation I'm getting
about a %20 decrease in the size of my .trr file from what it expects. 


>From my .out file for the molecular dynamics run I get 'WARNING: This run
will generate roughly 24940 Mb of data'

Actual amount of data produced is ~18 Gb of data. 

There are no errors running gmx_check on any of the tpr files are anything


I've tried running the same simulation on two different supercomputing
clusters to see if the same error occurs just in case it was an issue of the
build version having any effect on the size and run into the same problems

I've tried running the simulation in parts just in case there was some
memory issue causing some problem that I wasn't aware of or looking for

I've gotten my labmate and one more person familiar with GROMACS to look at
my issued commands and they seem stumped

I've also tried running it on 4.6.3 with the verlet cutoff scheme as I was
having some issues with pp/pme load balance


Nothing so far has made a difference and although the data seems to be fine
I'm loathe to do all the analysis if there is something majorly wrong with
my simulation. Problem for me is I don't know if or by how much the actual
trr file size should change from the expected amounts. 


Command submitted: mdrun_mpi -npme -1 -s MD.tpr -o MD.trr -x MD.xtc -c
MD.pdb -e MD.edr -g MD.log -v -dlb yes -cpo MD.cpt

I am running/wanting to run my simulations for 25 - 50ns


Thanks in advance for any help and all the best!







This email is free from viruses and malware because avast! Antivirus protection is active.

More information about the gromacs.org_gmx-users mailing list