Hi, You haven't said what you're trying to model, so it's going to be hard for someone to help out :-)
Mark On Thu, 10 Nov 2016 05:21 Abhi Acharya <abhi117acha...@gmail.com> wrote: > Thank you Stephane for your suggestion. Though this seems like a nice > solution to circumvent the problem, but do you think this is the normal way > to go about it? I have never found anyone reporting such a methodology for > membrane peptide simulation. Also, I can anticipate significant increase in > computational costs for a double bilayer system. I have a 800 lipid > molecules in a single bilayer, so this is significant factor for me. > > Thanks and Regards, > Abhishek > > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <stephane.a...@cea.fr > > > wrote: > > > Hi, > > > > it is not an issue !! To resolve your problem you could simulate two > > bilayer in box and insert the peptides between them. > > > > HTH > > > > ------------------------------ > > > > Message: 6 > > Date: Wed, 9 Nov 2016 16:07:26 +0530 > > From: Abhi Acharya <abhi117acha...@gmail.com> > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation > > Message-ID: > > <CAB1aw3zkCH7wmR6Za9H4OHm1PLG95cAeO0HJksxyxZi8yXC9Cg@mail. > > gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Dear Gromacs users, > > > > I am trying to simulate a system consisting of a lipid bilayer and few > > peptides. The peptides have been added randomly to the simulation box > only > > on one side of the membrane. I ran a 100 ns simulation of the system > using > > CHARMM36 forcefeild. However, I find that within the first few ns, some > of > > the peptides appear on the other side of the membrane. I think that this > is > > because of the diffusion of the peptides though the periodic boundary. > > Kindly suggest how to tackle this problem. I have used COM motion > removal > > on the whole system for the said simulation. > > > > Regards, > > Abhishek Acharya > > > > > > ------------------------------ > > > > -- > > 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. > > > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32 > > ****************************************************** > > -- > > 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.