[gmx-users] How to center my complex in the box?

ISHRAT JAHAN jishrat17 at gmail.com
Sat Aug 25 16:47:17 CEST 2018

Try -pbc mol and -ur compact with trjconv command. I think this will help.

On Sat, Aug 25, 2018 at 7:53 PM mmousivand93 <mmousivand93 at ut.ac.ir> wrote:

> Dear all users
> I have  run a molecular dynamic simulation for my aptamer-ligand  by
> gromacs (50 ns), At the end of simulations,by using VMD,it seems the
> molecule is out side the box, but I am not sure, is it possible to check
> the attachment and explain how to center it again?
> Thanks a lot
> Maryam--
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Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh

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