[gmx-users] PBC problem after MD

[kannan]

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...

regards
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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