[gmx-users] PBC problem after MD

[SEMRAN İPEK]

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