[gmx-users] trjconv and -pbc
tsjerkw at gmail.com
Fri Oct 28 05:48:40 CEST 2011
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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