Hello, How did you construct your membrane, with CHARMM-GUI? What is the lipid? From my experience, I have found that sometimes CHARMM-GUI does not provide a good starting point for MD. So I would suggest you to :
- center the lipids inside the box to have no lipids that cross the box limit and/or increase a little bit the box size (x-y) and minimize your system again. Moreover to insert you protein inside the membrane, did you try the inflate_gro or g_membed tools ? Good luck HTH ---------------------------------------------------------------------- Message: 1 Date: Sun, 16 Aug 2015 10:51:42 +0900 From: Vy Phan <phanvy120...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] infinite force at the membrane lipid Message-ID: <CAC+3Te00hidSrXE49g5mfqvCsBSaE5wTJ-NtFubaXvvz=u6...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear Dr Justin and Gromacs User, This is my commands for running energy minimization. define = -DPOSRES integrator = cg nstcgsteep = 1000 emtol = 100.0 emstep = 0.01 dt = 0.002 ; Output control nstxout = 50 nstenergy = 50 nstlog = 50 nstlist = 1 cutoff-scheme = Verlet ns_type = grid coulombtype = PME rcoulomb = 1.2 vdw-modifier = Potential-shift rvdw = 1.2 rvdw-switch = 1.0 pbc = xyz I hope you can give more recommendations. Removing lipids actually is not an appropriate solution. Thank you so much Tuong Vy 2015-08-16 1:47 GMT+09:00 Justin Lemkul <jalem...@vt.edu>: > > > On 8/15/15 12:41 PM, Vy Phan wrote: > >> Dear All gromacs Users, >> >> I want to run the membrane protein simulation. I run the energy >> minimization for membrane and protein separately. >> After that I combine protein and lipid together and remove the >> overlapping >> molecules. >> when I run energy minimization I got the error "inf at atom on lipid". I >> remove the lipid which includes this atom. I got the error several time >> and I repeat remove lipid. I see the "inf at atom on lipid" always happens >> on lipids which locate at the wall (at the boundary of unit cell). >> >> I successfully run one time when I remove lipids have error, another was >> failed. >> >> I wonder why the error "inf at atom on lipid" always happens on lipids >> which locate at the wall. Maybe I did something wrong about periodic >> boundary condition. >> >> Thank you for any thoughts. >> >> > Without a list of your exact commands and what you've done to this point, > it's impossible to diagnose. There's something fundamentally wrong with > the coordinates, topology, or both. If the infinite force is just moving > around, what you're observing is a symptom, not a cause, and removing > lipids to try to make it go away is not an appropriate solution. > > -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. End of gromacs.org_gmx-users Digest, Vol 136, Issue 75 ****************************************************** -- 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.