On 28/10/2011 2:39 PM, lina wrote:
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
<j.marzine...@imperial.ac.uk> wrote:
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of lina [lina.lastn...@gmail.com]
Sent: Thursday, October 27, 2011 10:47 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] trjconv and -pbc
Hi,
I have a problem using
trjconv_g -pbc nojump
or
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!
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions?highlight=pbc
Just use the trjconv -h to see each option.
Ha, I think I have tried those options. That's why I am confused.
Thanks,
Well, you need to try them better :) If you want your trajectory to keep
protein and something else together, you will need an index group that
combines them not jumping, and then combines them centering (or whatever).
Mark
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