[gmx-users] trjconv and -pbc

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Oct 28 05:48:40 CEST 2011

Hi Lina,

Make sure to use a reference in which the molecules are together (clustered)
the way you want them.



On Oct 27, 2011 11:47 AM, "lina" <lina.lastname at gmail.com> wrote:


I have a problem using

trjconv_g -pbc nojump

trjconv_g -pbc nojump -center

I even tried the -pbc whole.

The system is protein with a small molecular, for the first time
period, when I checked on pymol.
they are together, but later they apart, after show cell, protein
inside the cell, while this small molecular outside,

I did not meet such issue before, it's used  to be easy to fix the pbc
problem, but not this one. a bit surprise,

They are supposed to be together,

Thanks for any advice,
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