Re: [AMBER] Deleting Box info from trajectory

From: David A Case <>
Date: Sat, 14 Jun 2014 14:51:36 -0600

On Sat, Jun 14, 2014, Kshatresh Dutta Dubey wrote:
> I have a simulated a protein ligand complex using PBC, but for the
> purpose of QM/MM calculations I want to remove the box info from the
> trajectory 'without striping water'.

I'm not sure why one would want to do this. The same arguments that lead
to the use of PBC for explicitly solvated MM calculations apply with equal
force for QM/MM simulations.

You *can* get rid of box information by setting IFBOX=0 in the prmtop
header, and setting ntb=0 in your sander input file. But then the MM
energies will be quite different, and you will no longer be "equilibrated"
(to whateer extent you were before embarking on QM/MM.)

If you are convinced that you need a non-PBC environment for QM/MM, I'd
recommend doing the MM part the same way.


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Received on Sat Jun 14 2014 - 14:00:02 PDT
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