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

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Mon Aug 27 05:30:00 CEST 2018

    Did u properly minimized and equilibrated your system. If so....Then
the molecules out of the box may be the periodic images...You can use
trjconv to convert the trajectory to another unit cell...and check again

On Sat 25 Aug, 2018, 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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