Dear All, As I have introduced in my previous e-mail,
"After energy minimization and equilibrations, I am now running a 50 ns production MD, for a protein of 6 identical subunits, with each subunit about 300 residues (from resi 120 to resi 420), and there were no breaks in any chain. Every day it runs about 1 ns, and every day I use the command trjconv to get a new PDB based on the md_0_1.trr file, for the comparison between the new pdb and the initial pdb. Today I got the PDB at 6 ns. However when I checked it my pymol, I find there is something very strange. Although the rmsd between the 6 ns md PDB and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom away from this residues neighbouring residues, and correspondingly make chain B has a break at residue 366-367!" A moment ago by trjconv I regot the6 ns pdb with water, I find the residue 366-367 are almost (or exactly) at the edge of the water box (but by naked eye it seems the residue 366-367 are not outside of the water box). In this does the moving away of the residue 366-367 are still caused by " Periodic_Boundary_Conditions", and can I continue the production md to completion with the residue 366-367 disconnected from the major part of the protein complex and then I correct it by trjconv? I am looking forward to getting a reply from you. Brett -------- Forwarding messages -------- From: "Tsjerk Wassenaar" <tsje...@gmail.com> Date: 2016-04-14 12:16:56 To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> Subject: Re: [gmx-users] very strange phenomenon for my production MD by gromacs right! Cheers, Tsjerk On Apr 14, 2016 05:32, "Brett" <brettliu...@163.com> wrote: > Dear All, > > If the issue in my production MD was caused by > "Periodic_Boundary_Conditions", I can continue my production MD until it > completed, and it will not affect my final results suppose I have it > corrected by trjconv, right? > > > Brett > > > > > > > > > > > > At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > > >On 4/13/16 10:30 AM, Brett wrote: > >> Dear All, > >> > >> > >> After energy minimization and equilibrations, I am now running a 50 ns > >> production MD, for a protein of 6 identical subunits, with each subunit > about > >> 300 residues (from resi 120 to resi 420), and there were no breaks in > any > >> chain. Every day it runs about 1 ns, and every day I use the command > trjconv > >> to get a new PDB based on the md_0_1.trr file, for the comparison > between the > >> new pdb and the initial pdb. > >> > >> > >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find > there > >> is something very strange. Although the rmsd between the 6 ns md PDB > and 0ns > >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180 > angstrom > >> away from this residues neighbouring residues, and correspondingly make > chain > >> B has a break at residue 366-367! > >> > >> > >> Will you please let me know what is wrong with my MD, and why 2 residues > >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often > occur? > >> > > > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > >-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. > -- 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.