[gmx-users] PBC problem after MD

Mark Abraham mark.j.abraham at gmail.com
Thu Feb 13 12:23:20 CET 2014

If there's a problem, trjconv can handle it with the use of the right index
groups, as suggested at
But it can't keep "these three things" together if there's no index group
that describes "these three things." You may need to generate it with


On Thu, Feb 13, 2014 at 11:36 AM, SEMRAN İPEK <semranipek at gmail.com> wrote:

> Hi all,
> I am aware of that this topic has been discussed for many times. However, I
> need your more guidance  whether I am experiencing PBC problem after MD or
> not.
> My MD box has enzyme+ligand+coenzyme complex. As I have already wrote to
> the user list, I am using the force field parameters from literature for
> the ligand. And other paramaters related to MD has been checked twice.
> After MD what I have seen is that ligand is getting far away from the
> active site of the coenzyme.
> Justin has mentioned that this is the PBC problem (thank you Justin for
> your endless and comprehensive support.). Whatever I do was useless to cure
> the PBC problem.
> Could you please check my distance file showing the distance between ligand
> and coenzyme during MD simulation?
> And could you please share your experince if this is the PBC problem or
> not?if yes, why trjconvc can not handle it?
> Best Regards,
> --ipek
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