Dear Justin, Thank you for your advice.
I tried to restraint the wandering peptides, because umbrella MD results showed 'missing z=0.? ‘ errors when I run WHAM analysis. If I narrow the sampling space from 0.2nm to 0.1nm for umbrella MD simulation, could it be a better way to solve the ‘missing z=0.?’ errors than using position restraint to keep the wandering peptides in there position according to their initial z coordinates? Thanks again. Regards, Yoochan > On Sep 20, 2016, at 4:32 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/18/16 11:35 PM, Yoo Chan Myung wrote: >> Dear gmx users, >> >> I'm trying to simulate membrane penetration with peptide(octamer) using >> GROMACS-5.1.2. and I referred the Umbrella Sampling tutorial by Dr. Justin >> Lemkul. >> >> After 100 ps umbrella_NPT run, peptides confirmations are still kept in >> their initial coordinates. However, after 10ns of umbrella_MD, I cannot get >> reliable results for WHAM analysis because the confirmations are quite >> deviated from the umbrella_NPT structures. >> (plz, refer two results, >> https://www.dropbox.com/s/maqwjww8nozmcn6/q_a.jpg?dl=0) >> >> So, my question is should I have to use position restraint for moving >> ligands? or just extend simulation time for umbrella_NPT to get equilibrium >> structures for umbrella_MD? >> > > What would you restrain? Don't fall into the trap that many people seem to > do (despite me warning against it...) and try to follow the tutorial too > literally. Restraining the peptide in the tutorial had a specific purpose. > it's something that probably 99% of umbrella sampling simulations should NOT > use. > > Your structure is basically just falling apart. You may need some > inter-peptide restraints to preserve the geometry, but then deconvoluting all > of that into a meaningful PMF for just pulling the aggregate through the > membrane becomes very challenging. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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.
