[gmx-users] trjconv and -pbc

[Marzinek, Jan]

________________________________________
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

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.

Jan

===========================================================
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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