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

Fri Apr 15 16:30:17 CEST 2016

Hi,

On Fri, Apr 15, 2016 at 3:44 PM Brett <brettliu123 at 163.com> wrote:

> Dear Mark,
>
>
>
> My protein was a 6-identical subunit protein complex, initially each
> subunit contains a ligand. I want to see the conformational change from
> ligand bond to ligand free state, during this process there were reports
> that significant conformation change would occur
>
>
> First from the initial PDB with the ligands, I delete the ligands and get
> the apo pdb, after pdb2gmx etc, I process the energy minimization, nvt
> equilibration and npt equilibration, then I start the production md. During
> the initial 6 ns production md, there were some conformation change
> observed, but I do not know whether it diffuse.
>

You also have a large number of water molecules. The outermost extent of
their shape (their "envelope") was what you observed as becoming more
spherical, once you required their representation to avoid jumps over the
duration of the trajectory.

In addition, I do not understand what is "the envelope of the diffusion",

If you do a large number of one-dimensional random walks, you have a
characteristic distribution of the results, right? Here, your water
molecules are doing a three-dimensional random walk, without jumps. The
distribution of their final displacements isn't going to resemble your
starting shape. But if you choose a representation where they jump, then
the starting shape will remain.

and does diffusion leads the box from cubic to sphere?
>

Don't confuse the representation with what happened. You told mdrun to do a
periodic simulation. If you later require the representation of the
trajectory to not have jumps over boundaries, you aren't changing the
simulation.

Mark

Brett
>
>
>
>
>
>
>
>
>
> At 2016-04-15 21:30:12, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> >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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> >> >> >>> --
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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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