[gmx-users] g_msd problem

[Justin Lemkul]

On 5/18/13 4:32 PM, rajat desikan wrote:
> I have experienced something similar with large trajectories.
>
> This command got killed by 42 ns, with the same error. It is a 60 ns
> trajectory of a large membrane-protein system (approx 450000 particles,
> Gromos 54A7 ff) with data stored every ps.
>
> g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tpr -o
> msd_popc_overall.xvg -lateral z -n index.ndx
>
>

Both issues sound like memory problems.  See 
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume 
for advice.  If reducing the number of frames allows the program to run 
successfully, you have your answer.

In the OP's case, I would advise upgrading from version 4.0.3, which is ancient. 
  At the very least, try 4.0.7, which is the terminal version in the 4.0.x 
series.  Development is fluid and small bugs get fixed all the time, so using a 
version that is more than 4 years old may be asking for trouble.

-Justin

> On Sun, May 19, 2013 at 1:57 AM, Yutian Yang <yyang18 at syr.edu> wrote:
>
>> Dear all,
>>
>> I am using g_msd to calculate diffusion coefficient of the centre of mass
>> of single polymer chain with the following command:
>> g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 50000 -endfit
>> 400000
>>
>> However, it often get killed for number of beads larger than 37, as shown
>> below:
>>
>> Reading file eqm.tpr, VERSION 4.0.3 (single precision)
>> Reading file eqm.tpr, VERSION 4.0.3 (single precision)
>>
>> Select a group to calculate mean squared displacement for:
>> Group     0 (         System) has 13042 elements
>> Group     1 (            PEO) has    37 elements
>> Group     2 (             WF) has  1301 elements
>> Group     3 (              W) has 11704 elements
>> Group     4 (           WF_W) has 13005 elements
>> Select a group: 1
>> Selected 1: 'PEO'
>>
>> Now select a group for center of mass removal:
>> Group     0 (         System) has 13042 elements
>> Group     1 (            PEO) has    37 elements
>> Group     2 (             WF) has  1301 elements
>> Group     3 (              W) has 11704 elements
>> Group     4 (           WF_W) has 13005 elements
>> Select a group: 1
>> Selected 1: 'PEO'
>> trn version: GMX_trn_file (single precision)
>> Reading frame   24000 time 240000.000   Killed.
>>
>> Is it also a bug in the program or have I done something wrong on the
>> command?
>>
>> Thank you!
>>
>> Best Regards
>> Yutian Yang
>>
>>
>>
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================