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

Mark Abraham mark.j.abraham at gmail.com
Fri Apr 15 15:30:24 CEST 2016 

Hi,

On Fri, Apr 15, 2016 at 3:18 PM Brett <brettliu123 at 163.com> wrote:

> Dear All,
>
> By xmgrace I have checked the xmgrace, I find the spike was between
> -8.245e+06 and -8.225e+06, is the spike massive or not?
>
>
> In addition, by
> gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc
> nojump -dump 6000,
>
>
> I got the 6 ns with water pdb and I have checked the pdb (with water box),
> I find the resi 366-367 were not disconnected!
>
>
> However, by gmx editconf, the original water box was in cubic, after "gmx
> trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump
> -dump 6000", the cubic water box was replaced by a rough sphere water box
> with the protein roughly in the center. Will you please explain why the
> cubic water box was replaced by the round sphere water box? Anything wrong
> I have made?
>

You've simulated a bunch of molecules that diffuse. What shape would you
expect for the envelope of the diffusion? How would it vary over time?

Further, by visual check if in a production MD I did not see residue
> disconnection caused by "Periodic_Boundary_Conditions", can we guarantee no
> minor disconnection occurred during the md (or significant bond length
> variance unobservable by the naked eye with pymol) if we did not process
> the trjconv correction step?
>

The forces produced by such a disconnection would blow everything up
immediately. Since it didn't...

Mark


> I am looking forward to getting a reply from you.
>
>
> Brett
>
>
>
>
>
>
> At 2016-04-14 20:02:43, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> >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
> >> >>>>>
> >> >>>>> ==================================================
> >> >>>>> --
> >> >>>>> Gromacs Users mailing list
> >> >>>>>
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> >> >>>> posting!
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> >> >>>>>
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> >> >> --
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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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> >--
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