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

Brett brettliu123 at 163.com
Fri Apr 15 15:17:47 CEST 2016 

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?


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?


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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>> --
>> ==================================================
>>
>> 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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