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

[Chandan Choudhury]

On Wed, May 21, 2014 at 6:37 PM, Vito Genna <Vito.Genna at iit.it> wrote:

> 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.
>
>
It seems that the tpr you are supplying has PBC in it. I assume the first
tpr should be generated from PBC free structure. That is the understanding
I had.
Correct me if I am wrong.

Chandan

> 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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-- 

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India