Re: [gmx-users] REMD simulation of peptide-membrane system
On 03/03/11, Jianguo Li wrote: > > > > > > Dear all, > > I'd like to do folding simulations of a short peptide on membrane surface > using REMD using atomistic FF. But the problem is that membrane will disrupt > at high temperatures. To maintain the membrane structure, I am thinking the > following two methods: > > (1) To use different coupling temperature for different groups (e.g., keeping > membrane at 323K for all the replicas, but keeping peptide and water with > different temperatures). Will this lead to artifact? > > > > > Yes. You will have heat flowing via the system between two external heat baths. > > > > > (2) If this leads to serious artifact, I may need to use constraints on the > membrane, as mentioned in the paper from Berkowitz group. > > > > > That seems more wise, but still not great. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] REMD simulation of peptide-membrane system
Dear all, I'd like to do folding simulations of a short peptide on membrane surface using REMD using atomistic FF. But the problem is that membrane will disrupt at high temperatures. To maintain the membrane structure, I am thinking the following two methods: (1) To use different coupling temperature for different groups (e.g., keeping membrane at 323K for all the replicas, but keeping peptide and water with different temperatures). Will this lead to artifact? (2) If this leads to serious artifact, I may need to use constraints on the membrane, as mentioned in the paper from Berkowitz group. Is there any other method for the above problem? Any comments is greatly appreciated, thank you in advance, Cheers, Jianguo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
