What I meant to ask was a way to ensure that the peptides and membrane COM don't drift out of the simulation box, but the peptides should be free to move ( relative to the membrane) within the box. Basically, the best way to simulate the diffusion and subsequent interaction of the peptides with the lipid membrane.
What I can surmise from previous similar studies is that creating separate comm groups for Membrane, solute and ion and the peptide should be the correct way. Also, I wanted to know how different nstcomm values would effect the result especially in the context of complex systems such as this. Just wanted to be sure, before I start the production runs. On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund <erik.markl...@kemi.uu.se> wrote: > > > On 27 Sep 2016, at 06:26, Abhi Acharya <abhi117acha...@gmail.com> wrote: > > > > Dear Gromacs users, > > > > I am trying to perform a simulations of different concentration of > peptides > > in a box with lipid bilayer. In this context, I had a query regarding the > > correct Center-of-Mass removal settings; what would be the correct way to > > ensure that the Membrane is stationary during long simulations while the > > peptides, solutes etc freely diffuse in the box. Based on my > understanding, > > I am using the following settings in the parameter file: > > > > nstcomm = 100 > > comm_mode = linear > > comm_grps = MEMB SOL_ION Peptide > > > > Here the Peptide group includes a total of say 16 peptides. Would this be > > the correct way to perform the simulation? > > > > Is is possible to set individual nstcomm values for each group so as to > > ensure that the peptides diffuse freely while the membrane stays > stationary? > > Why do you want that in the first place? Membranes aren’t stationary. > > Kind regards, > Erik > > > > > The full mdp settings I intend to use is provided in the following link: > > > > https://drive.google.com/file/d/0B9VrCGta6IxES3NHU3lRbGJ4d00/ > view?usp=sharing > > > > Please advise of what would be the best settings to perform the > simulation. > > > > Best Regards, > > Abhishek Acharya > > C-CAMP > > Bangalore. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.