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

[Tsjerk Wassenaar]

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.