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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 21 13:48:55 CEST 2014

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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