[gmx-users] PBC problem after MD

kannan kannan.2910 at gmail.com
Thu Feb 13 12:24:39 CET 2014

Hi ipek,
Handlind trjconv for complex is critical,but possible.. if you want to know
whether the ligand is bind with protein or no, you could do some analyse
part such as h-bond...

kannan s

On Thu, Feb 13, 2014 at 4:13 PM, ipek [via GROMACS] <
ml-node+s5086n5014519h36 at n6.nabble.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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