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

Vito Genna Vito.Genna at iit.it
Wed May 21 16:11:23 CEST 2014

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.


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?



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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