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

[Tsjerk Wassenaar]

That doesn't make sense..., sorry.

Cheers,

Tsjerk
On May 21, 2014 6:40 PM, "Chandan Choudhury" <iitdckc at gmail.com> wrote:

> 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
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