Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the "centre of mass removal" component in my .mdp file (which we do for an all-atom protein + lipid simulation)? Should I use the below given parameters in my mdp file for this CGMD simulation:
------------------------------------------------------------------------------------------------- ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DSPC W ------------------------------------------------------------------------------------------------- Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
