[gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Tue May 20 21:37:56 CEST 2014

Hi Vito,

If the .tpr file is good, i.e. has everything assembled the way you want,
then the first step is trjconv -pbc nojump. That will make sure that
nothing gets split over PBC. Then center the protein in the box (trjconv
-center), and subsequently put all molecules in the box (-pbc mol -ur
compact/rect).

Cheers,

Tsjerk

On Tue, May 20, 2014 at 7:51 PM, Vito Genna <Vito.Genna at iit.it> wrote:

> Hi Tsjerk,
>
> Thank you for your email.
> No it is not broken. The structure is intact till the 20 ns of production
> phase.
> I have already used the .tpr (both md_0_1.tpr before, and then npt.tpr)
> obtaining the same result.
> Basically you are suggesting to fix the first frame of the production
> phase and use it as a reference point
> for the subsequent manipulations (-pbs nojump) of all TRJs?
> I'm going to do this attempt and I will keep you posted.
>
> Thanks again.
>
> Cheers
>
> V
>
> Vito Genna, PhD-Fellow
> Italian Institute of Technology
> Drug Discovery and Development department
> Via Morego 30, 16163 Genoa, Italy
>
>
> -------------------------------------------------------------------------------------------------------------
> The process of scientific discovery is, in effect, a continual flight from
> wonder.
> Albert Einstein
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Tsjerk
> Wassenaar [tsjerkw at gmail.com]
> Sent: Tuesday, May 20, 2014 7:30 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> for VMD using
>
> Hi Vito,
>
> Was the structure already broken up when you solvated it? If not, which
> seems likely to me, then you can use that structure, or the .tpr from the
> EM in solvent, to remove jumps from the first frame of your run. After you
> unbroke the first frame, you can use that as reference for processing your
> trajectory with -pbc nojump.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Tue, May 20, 2014 at 7:14 PM, Vito Genna <Vito.Genna at iit.it> wrote:
>
> > Dear Justin,
> >
> > Thank you for your email.
> > As in your case, my system is formed by a Protein + dsDNA + structural
> > ions + counterions + ligand + water
> > I guess that I have too much element to efficiently solve the problem but
> > I want to try to fix it. The solution could help
> > other people to avoid to became crazy with this kind of TRJs
> manipulations.
> >
> > Figs. link: http://wikisend.com/download/571570/pics.zip
> >
> > Well. today I tried  a different combo as:
> >
> >  A) trjconv -s -f -pbc mol(res) -center (-n index with
> > DNA&Protein/Ligand/Protein)
> >
> > to obtain trajectories as shown in pic1
> >
> > B) Then i used -pbc whole/nojump to obtain a result as shown in fig 2
> >
> > I guess that the problem still persists....
> >
> > Any suggestion about your experience?
> >
> > Thanks in advance
> >
> > V
> >
> > Vito Genna, PhD-Fellow
> > Italian Institute of Technology
> > Drug Discovery and Development department
> > Via Morego 30, 16163 Genoa, Italy
> >
> >
> >
> -------------------------------------------------------------------------------------------------------------
> > The process of scientific discovery is, in effect, a continual flight
> from
> > wonder.
> > Albert Einstein
> >
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin
> > Lemkul [jalemkul at vt.edu]
> > Sent: Monday, May 19, 2014 11:26 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> > for VMD using
> >
> > On 5/19/14, 12:29 PM, Vito Genna wrote:
> > > Dear Mark,
> > >
> > > You can see the results of -pbc whole and -pbc nojump on this pics
> > http://wikisend.com/download/777550/PICs.zip
> > > I tried to use the flag -s with the .tpr and then with the .gro file
> but
> > in both cases I obtain a result similar to that one shown on
> > > PICs on link. A broken system.
> > > Both .tpr and .gro used for the -pbc whole/nojumo/fit are ok and the
> > system is complete.During the equillibration and for the first ~20ns of
> > production phase
> > > the system is stable within the box. The problem start to appear as
> soon
> > as the system leaves the first box (~25ns)
> > >
> >
> > Can you post an image looking straight-on at the system, with box vectors
> > rendered, with and without water?  The oblique shots you've provided are
> a
> > bit
> > hard to interpret.
> >
> > I've dealt with very complex systems like these (multiple proteins +
> dsDNA
> > +
> > ions + ligands) and it is a pain.  I believe I went through 6 rounds of
> > trjconv
> > for most of them (hundreds of ns in length).  The exact protocol is
> highly
> > system-specific, but the key is that it is often necessary to use custom
> > index
> > groups (a specific residue, or a few in some key location) for centering
> > and/or
> > fitting.
> >
> > -Justin
> >
> > > Thanks in advance
> > >
> > > V
> > >
> > > Vito Genna, PhD-Fellow
> > > Italian Institute of Technology
> > > Drug Discovery and Development department
> > > Via Morego 30, 16163 Genoa, Italy
> > >
> > >
> >
> -------------------------------------------------------------------------------------------------------------
> > > The process of scientific discovery is, in effect, a continual flight
> > from wonder.
> > > Albert Einstein
> > >
> > >
> > > ________________________________________
> > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> > Abraham [mark.j.abraham at gmail.com]
> > > Sent: Monday, May 19, 2014 5:32 PM
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
> > problems for VMD using
> > >
> > > On Mon, May 19, 2014 at 5:03 PM, Vito Genna <Vito.Genna at iit.it> wrote:
> > >
> > >> Dear Mark,
> > >>
> > >> Thank you for you prompt reply.
> > >> Yes, indeed I was following the suggested trjconv workflow. Right you
> > are.
> > >> When I say "does not work" I mean that the system is stretched between
> > two
> > >> adjacent boxes showing internal bonds that run throughout the "main"
> pbc
> > >> box (extremely long).
> > >>
> > >> Regarding the steps:
> > >> Yes I already visualized the results step by step and after the 1) one
> > >> trjconv fixes the bond problems but splits my protein in two distinct
> > part
> > >> (the protein contains only 1 chain) moving them in two boxes.
> > >>
> > >
> > > Sounds like you mean trjconv from your 1)a). Please be specific. If so,
> > > IIRC, -pbc whole restores the "wholeness" as it judges from state of
> the
> > -s
> > > input. So if you made the .tpr from a .gro file that had the protein in
> > two
> > > chunks across periodic boundaries from the equilibration, so will the
> > > output be split. This was what I guessed before, but you didn't report
> > > whether you investigated whether your .tpr file contained what you
> think
> > it
> > > does. IIRC you can also use a coordinate file for -s for that stage,
> > since
> > > "-pbc whole" does not actually use the topology, and it is easier to
> > > construct a .gro file that looks how you want.
> > >
> > > Mark
> > >
> > > At this point I use the -pbc nojump option that gives me the same
> > previous
> > >> problem (bond excessively long).
> > >>
> > >> If I could reassembly the protein after -pbc whole action I'll be
> > >> completely satisfied.
> > >>
> > >> Any suggestion?
> > >>
> > >> Thank in advance.
> > >>
> > >> Cheers
> > >>
> > >> Vito Genna, PhD-Fellow
> > >> Italian Institute of Technology
> > >> Drug Discovery and Development department
> > >> Via Morego 30, 16163 Genoa, Italy
> > >>
> > >>
> > >>
> >
> -------------------------------------------------------------------------------------------------------------
> > >> The process of scientific discovery is, in effect, a continual flight
> > from
> > >> wonder.
> > >> Albert Einstein
> > >>
> > >>
> > >> ________________________________________
> > >> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> > >> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Mark
> > >> Abraham [mark.j.abraham at gmail.com]
> > >> Sent: Monday, May 19, 2014 4:31 PM
> > >> To: Discussion list for GROMACS users
> > >> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
> > problems
> > >> for VMD using
> > >>
> > >> You seem to be following
> > >>
> > >>
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> > >> ,
> > >> which is good. But it's hard to help when we don't know what you think
> > >> "doesn't work" means. Make sure that the things you think are whole in
> > >> md_0_1.tpr actually are. Visualize your intermediate stages of 1) to
> see
> > >> where the issue arises. If you need to, upload some pictures to a file
> > >> sharing service that show what the input and unsatisfactory output
> was.
> > >>
> > >> Mark
> > >>
> > >> On Mon, May 19, 2014 at 3:15 PM, Vito Genna <Vito.Genna at iit.it>
> wrote:
> > >>
> > >>> Hi to everybody,
> > >>>
> > >>> My name is Vito and I would like to share with you (and discuss also)
> > the
> > >>> problems that I have found during my TRJs analysis.
> > >>> I have a system made by: Protein + dsDNA + Ligand. I obtained my
> single
> > >>> precision trajectory in a .xtc file.
> > >>> Well, I'd like to analyze my TRJs using VMD due to its intrinsic
> > velocity
> > >>> in calcuating (Distances, angles, RMSD and so on) but I cannot do it
> > >>> because I encounter a serious issue with the visualization (pbc
> > problems
> > >> as
> > >>> you surely know)
> > >>> To try to avoid the problem I've used several protocols, without
> > success:
> > >>>
> > >>> 1)
> > >>>
> > >>> a) trjconv_mpi -f md_0_1.part0001.xtc -o md_0_1-whole.xtc -s
> md_0_1.tpr
> > >>> -pbc whole (on the entire system)
> > >>> b) trjconv_mpi -f md_0_1-whole.xtc -o md_0_1-nojump.xtc -s md_0_1.tpr
> > >> -pbc
> > >>> nojump
> > >>> (on the entire system)
> > >>> c) trjconv_mpi -f md_0_1-nojump.xtc -o md_0_1-fit.xtc -s md_0_1.tpr
> > -fit
> > >>> progressive (on Protein only)
> > >>>
> > >>> It does not work.
> > >>>
> > >>> 2)
> > >>>
> > >>> a) trjconv_mpi -f (as the previous one) -pbc mol -ur compact -center
> -o
> > >>> compact.xtc
> > >>>
> > >>> It does not work as well.
> > >>>
> > >>> 3) Option 2 changing the flag -pbc mol with -pbc res
> > >>>
> > >>> It does not work.
> > >>>
> > >>> New idea? New possible combo?
> > >>>
> > >>> Thanks in advance for your replies.
> > >>>
> > >>> All the best
> > >>>
> > >>> Vito
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> Vito Genna, PhD-Fellow
> > >>> Italian Institute of Technology
> > >>> Drug Discovery and Development department
> > >>> Via Morego 30, 16163 Genoa, Italy
> > >>>
> > >>>
> > >>>
> > >>
> >
> -------------------------------------------------------------------------------------------------------------
> > >>> The process of scientific discovery is, in effect, a continual flight
> > >> from
> > >>> wonder.
> > >>> Albert Einstein
> > >>>
> > >>> --
> > >>> 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 601
> > 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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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.