[gmx-users] PBC problem after MD

SEMRAN İPEK semranipek at gmail.com
Thu Feb 13 12:25:38 CET 2014

Opps sorry. this is  the link for downloading my dist.jpeg file.


Thanks again.


2014-02-13 12:36 GMT+02:00 SEMRAN İPEK <semranipek at gmail.com>:

> 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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