[gmx-users] trjconv and -pbc

Marzinek, Jan j.marzinek10 at imperial.ac.uk
Thu Oct 27 12:11:29 CEST 2011

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of lina [lina.lastname at gmail.com]
Sent: Thursday, October 27, 2011 10:47 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] trjconv and -pbc


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,

I am sure it will help. Follow the workflow!


Just use the trjconv -h to see each option.


Jan Marzinek
PhD Candidate
Centre for Process Systems Engineering
Department of Chemical Engineering
Imperial College London
South Kensington Campus
London SW7 2AZ
E: j.marzinek10 at imperial.ac.uk
M: +44(0)7411 640 552

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