[gmx-users] g_msd problem

[Yutian Yang]

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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