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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 22 16:08:02 CEST 2014 

Hey Vito,

Don't use -skip. And add -pbc nojump to that first run of trjconv:

trjconv_mpi -f md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -pbc nojump

Then have a look at the last frame to see if it's good. If md_0_1.tpr is
assembled properly, then the last frame should be too, provided the
assembly did not fall apart (in which case you're in real trouble).

Cheers,

Tsjerk



On Thu, May 22, 2014 at 3:01 PM, Vito Genna <Vito.Genna at iit.it> wrote:

> Dear Tsjerk,
>
> I exactly executed: editconf -f npt.tpr -o npt.pdb and I obtained a nicely
> assembled system (npt.pdb).
>
> Well, my system start to cross the boundaries after 20 ns of production
> phase so the npt.tpr is not
> the first frame of the trajectories that I trying to fix.
>
> After your email I've generated the md_0_1.tpr respecting your request
> with the command  editconf -f md_0_1.tpr -o md_0_1.pdb
> and again I obtain a well assembled system.
>
> The trajectories that I want to fix, is obtained from: trjconv_mpi -f
> md_0_1.part0001.xtc -o test.xtc -s md_0_1.tpr -skip 100
>
> To be consistent in the procedure, I did again all the steps (-pbc nojump,
> -center, -compact -ur rect) using the md_0_1.tpr.
>
> The result is exactly the same! I'm really losing hope!
>
> I will try the Pymol strategy also.
>
> Thank you for your hints.
>
> 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: Thursday, May 22, 2014 11:10 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> for VMD using
>
> Hi Vito,
>
> Does npt.tpr correspond to the first frame of the trajectory and is the
> structure in npt.tpr correctly assembled? (editconf -f npt.tpr -o
> npt.tpr.pdb, and check). The only way that -pbc nojump can give a final
> frame in which the complex is separated is if the reference structure has
> them already separated. In that case, nothing you'll try will give you what
> you want. What I do in such cases is dump the first frame, using -pbc
> whole, and then shift the chains in Pymol according to the box vectors to
> have them together. Then I use the resulting structure as reference for
> processing the trajectory.
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, May 22, 2014 at 10:59 AM, Vito Genna <Vito.Genna at iit.it> wrote:
>
> > Dear Dr. Warrem, Dear Tsjerk,
> >
> > Thank you for your emails.
> > Following the suggestion of Dr. Warren I created several dir in which I
> > applied different protocols on my system
> >
> > -- DIR1 --
> >
> >  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
> >  (output System)
> >
> >  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> > -n iindex.ndx (centering all the frames on Protein)   (output system)
> >
> >  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc
> mol
> > -ur rect (output System)
> >
> > The related Figures are in the following link:
> > http://wikisend.com/download/832038/Figtest1.zip
> >
> > #Comment: I obtain the same result also if a change rect with compact in
> > the third step.
> >
> > -- DIR2 --
> >
> >  1) trjconv_mpi -s npt.tpr -f test.xtc -o test-nojump.xtc -pbc nojump
> >  (output System)
> >
> >  2) trjconv_mpi -s npt.tpr -f test-nojump.xtc -o test-center.xtc - center
> > -n iindex.ndx (centering all the frames on Protein)   (output system)
> >
> >  3) trjconv_mpi -s npt.tpr -f test-center.xtc -o test-compact.xtc -pbc
> mol
> > -ur rect (output System)
> >
> >  4) trjconv_mpi -s npt.tpr -f test-compact.xtc -o test-fit.xtc -fit
> > progressive (fitting on Protein)
> >
> > The pics are here: http://wikisend.com/download/615140/FigTest2.zip
> >
> > #Comment: Here again, I obtain the same results as in the DIR1 but My
> > protein has not translational motions.
> > #Comment: In the step 2 i also centered the system on the Protein_DNA,
> > nothing changes.
> >
> >
> > Then, I tried different pbc/centering combination again but I strongly
> > believe that fixing DNA-Protein complex is enough to obtain a good
> system.
> >
> > What would do you do to bring back the dsDNA inside the protein?
> > In which step would you operate your command?
> >
> > Thanks in advance for your time.
> >
> > 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 Dallas
> > Warren [Dallas.Warren at monash.edu]
> > Sent: Thursday, May 22, 2014 1:40 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories problems
> > for VMD using
> >
> > Would suggest that each time you try a different workflow, do so in a new
> > subdirectory and copy the required files into there.  That way you ensure
> > are using the files you think that you are.
> >
> > Will help those assisting to then post an image of the coordinate files
> at
> > each step of the work flow, to see how things are changing, or not.
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.warren at monash.edu
> > +61 3 9903 9304
> > ---------------------------------
> > When the only tool you own is a hammer, every problem begins to resemble
> a
> > nail.
> >
> > > -----Original Message-----
> > > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > > [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf
> Of
> > > Vito Genna
> > > Sent: Wednesday, 21 May 2014 11:07 PM
> > > To: gmx-users at gromacs.org
> > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
> > > problems for VMD using
> > >
> > > Dear Tsjerk,
> > >
> > > No, it doesn't. (http://wikisend.com/download/324888/Post-nojump.png)
> > > I think that the first step need to be changed that's why I tried (whit
> > > no success)
> > > the flag -pbc whole. I'm still looking for a solution.
> > >
> > > Thanks again.
> > >
> > > 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 1:48 PM
> > > To: Discussion list for GROMACS users
> > > Subject: Re: [gmx-users] How to efficiently fix pbc trajectories
> > > problems for VMD using
> > >
> > > Hey Vito,
> > >
> > > After the first step, does the trajectory (say the last frame) look
> > > fine?
> > > If it does (everything nicely assembled), then after the second step,
> > > does
> > > it still look fine, and is it placed properly in the center of the box?
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > >
> > > On Wed, May 21, 2014 at 12:50 PM, Vito Genna <Vito.Genna at iit.it>
> wrote:
> > >
> > > > 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
> > > >
> > > >
> > > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

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