Dear HTH and Gromacs Users, Thank you HTH,
I used the DOPC membrane lipid pdb file and topology from the website http://mmkluster.fos.su.se/slipids/Downloads.html. I running energy minimization for protein in water and lipid in water. After that, I put the protein into the center of membrane lipid and use tcl script to remove all overlapping moleculas by this script. [atomselect 0 " resname DOPC and (same residue as resname DOPC and x >25 and x<110 and y > 20 and y < 115) and not (same residue as resname DOPC and within 1 of protein)"] writepdb DOPC.pdb [atomselect 0 " water and (same residue as water and x > 20 and x<115 and y > 15 and y < 120) and not (same residue as water and within 1 of protein)"] writepdb wat.pdb After that I combine protein, lipid and water to one system and run. I did not use inflate_gro or g_membed tools. The g_membed tools can not used in Gromacs 5 (I use Gromacs 5.0.4) Hope you can see my problems and help me more. If you think the way I insert the protein on the lipid is the problem. Please let me know. I usually do this way with NAMD. Best regards, Tuong Vy 2015-08-16 20:21 GMT+09:00 ABEL Stephane 175950 <stephane.a...@cea.fr>: > 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. > -- 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.
