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

Vito Genna Vito.Genna at iit.it
Wed May 21 12:51:01 CEST 2014 

Hi Tsierk,

Ok.

1) trjconv_mpi -s em.tpr -f test.xtc -o test-nojump.xtc -pbc nojump (output System)

2) trjconv_mpi -s em.tpr -f test-nojump.xtc -o test-center.xtc -center -n index.ndx (centering all the frames on different targets Protein/DNA ecc ecc) (output system)

3) trjconv_mpi -s em.tpr -f test-center.xtc -o test-compact.xtc -pbc mol -ur rect[or compact] (output System)

I also tried, successively, the same procedure adding one step more: -pbc whole
This last step was added before the step 1.

But at the end I obtain the same result.

Surely, I'm doing something wrong but I'm not understand what is wrong...:/

Thank you for your time.

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: Wednesday, May 21, 2014 11:58 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hey Vito,

Can you paste your exact workflow?

Cheers,

Tsjerk


On Wed, May 21, 2014 at 9:53 AM, Vito Genna <Vito.Genna at iit.it> wrote:

> Hi Tsierk,
>
> Hi tried your protocol without success.
> I have also tried different centering combination (on
> protein/DNA/Ligand/Protein+DNA/DNA+Ligand/Protein+ligand)
> and different flags combo (-pbc mol -ur compact/rect).
> I have added also the pbc whole before -pbc nojump but the result at the
> end is always the same, as shown in fig
> http://wikisend.com/download/185858/fig5.png
> The bonds are disappeared it's a god start but it is not enough to make
> measurements inside the catalytic pocket.
>
> I hope to find a solution with you and to write down a protocol for people
> which work whit ternary complexes.
>
> Thank you for your time.
>
> Best Regards
>
> 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 9:37 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> for VMD using
>
> 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
> > > >>>
> > > >>> * Please search the archive at
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> > > >>> posting!
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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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