Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal?
Regards, Anirban On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote: > > 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 >> >> ------------------------------------------------------------------------------------------------- >> > This is the way to go :)) > >> >> Any suggestion is welcome. Thanks a lot in advance. >> >> >> Regards, >> >> Anirban >> -- >> 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/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/mailing_lists/users.php >> > > -- > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- 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/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/mailing_lists/users.php
