[gmx-users] PBC problem after MD

[Mark Abraham]

If there's a problem, trjconv can handle it with the use of the right index
groups, as suggested at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
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
make_ndx.

Mark


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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