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
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
Dear Kannan,
Thank you for your fast response. The problem is that the ligand is as far
as 16 Ang., which is too far away from the coenzyme for any kind of bonding.
here is the link for downloading my dist.jpeg file.http://we.tl/ACencjievC
Do you think that this is a real PBC problem?
Really
