[gmx-users] g_msd problem

[rajat desikan]

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


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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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore