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

[Vito Genna]

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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