[gmx-users] very strange phenomenon for my production MD by gromacs

Thu Apr 14 14:02:59 CEST 2016

Hi,

If this "separation" was real, would you have expected to see

a) a massive spike in the potential energy
b) complete inability for the constraint algorithm to enforce bond lengths?

Hint, you haven't seen that.

Mark

On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/14/16 5:35 AM, Brett wrote:
> > Dear All,
> >
> >
> >
> > Thanks the reply.
> >
> >
> > But I think I need to discuss with you further on whether I need to
> discontinue my production MD. As I mentioned, resi 366-367 separated from
> the major body of the protein. By pymol I find resi 366-367 were at one
> edge of the box and were almost outside of the water box, and its
> neighbouring residues resi 365 and resi 368 were at the opposite edge of
> the box and were also almost outside of the water box.
> >
> >
> > It seems that way, although at the initial step by editconf I have put
> the protein in the center of the cubic box (1.5 nm), during the first 6 ns
> the protein has moved significantly in the box, and at some moment resi
> 366-367 have moved out of the box, leading to the disconnection of resi
> 366-367 from the major body of the protein and finally leading to resi
> 366-367 at the opposite of  its neighbouring residues resi 365 and resi 368
> in the cubix box.
> >
> >
> > Am I right?
> >
>
> Diffusion is normal.  The residues are not actually disconnected.  You can
> use
> trjconv to "fix" this state, but there is nothing physically wrong with it.
> mdrun cares about physics, not our visualization convenience.
>
> -Justin
>
> >
> > Brett
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > At 2016-04-14 16:31:20, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> >> Hi,
> >>
> >> As the link Justin gave you says, and Tsjerk has since confirmed, this
> is
> >> normal. There are infinitely many equivalent representations of your
> >> simulation, not all of which will look connected for the thing that is
> of
> >> interest.
> >>
> >> Strategies for handling visualisation are also on that link, but you
> don't
> >> need to handle anything within the simulation.
> >>
> >> Mark
> >>
> >> On Thu, 14 Apr 2016 09:48 Brett <brettliu123 at 163.com> wrote:
> >>
> >>> 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" <tsjerkw at gmail.com>
> >>> Date: 2016-04-14 12:16:56
> >>> To:  "Discussion list for GROMACS users" <gmx-users at 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" <brettliu123 at 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" <jalemkul at 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
> >>>>>
> >>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>>
> >>>>> ==================================================
> >>>>> --
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> --
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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