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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
