Dear Marius,
Thank you for your quick response.
I tried your suggestions for the workflow, it took me some time to understand making an index file for the last atom in the acyl chain.
Just wanted to check with you if I am doing it right. I did the following:
1. Making index group with an atom in the middle of the bilayer
gmx make_ndx -f …/step5_input.pdb -o CenterAtom.ndx
a C218 | a C316 # (selected atom C218 | atom C316 (which are at the end of POPE and POPG))
2. Centering for the selected atoms
gmx trjconv -s …/step7_1.tpr -f …/step7_1.trr -o step7_1_pbc_0_atom_trial10.xtc -pbc atom -tu ns -center -n CenterAtom.ndx # selected new group created by index above (C218_C316) for centering and ‘system’ for output
3. Making an index group with the whole bilayer e.g. Bilayer.ndx
gmx make_ndx -f …/step5_input.pdb -o Bilayer.ndx
“POPG” | “POPE” # Selecting both POPG and POPE
4. Centering for the selected mol (i.e. bilayer)
gmx trjconv -s …/step7_1.tpr -f step7_1_pbc_0_atom_trial10.xtc -o step7_1_pbc_0_mol_trial10.xtc -pbc mol -tu ns -center -n Bilayer.ndx # Selected POPG_POPE group created above
5. Visualization
vmd …/step7_1.gro step7_1_pbc_0_mol_trial10.xtc
And this worked, this time bilayer (POPG and POPE) are together during the whole run.
The only problem left now is that protein is jumping around, I guess need to use nojump using the step7_1_pbc_0_mol_trial10.xtc, without any index file?
Again, thanks a lot for your help. This was driving me crazy.
Sanjiv Kumar