[gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

[rajat desikan]

Hi All,
I have a few older membrane simulations for which the COM for the upper and
lower leaflets were not removed in the course of the simulations. These are
pretty long simulations exceeding 300 ns.
I have trouble with post-processing of the trajectory.
To remove the COM of the upper and lower leaflets separately, I executed
the following series of commands (shown for upper only):

Selecting upper leaflet:
g_select -s .tpr -on upper_P8.ndx -select 'resname DPPC and name P8 and
res_com z>4.3'
trjconv -f .gro -s .gro -n upper_P8.ndx -o test_u_P8.pdb  .........Testing
selection, everthing ok

Trajectory:
trjconv -f .xtc -s .tpr -n upper_P8.ndx -o upperP8_center_pbcnojump.xtc
-center -b 20000 -pbc nojump

MSD:
g_msd -f upperP8_center_pbcnojump.xtc -s .tpr -o msd_dppc_x_u.xvg  -type x
-n upper_P8.ndx

Select a group to calculate mean squared displacement for:
Group     0 (resname_DPPC_and_name_P8_and_res_com_z>4.3_0.000) has   192
elements
There is one group in the index
Reading frame      60 time 20600.000   Segmentation fault (core dumped)

Any ideas? Is there anything wrong with my workflow?

Thanks.

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