Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?)

From: David A Case <>
Date: Fri, 22 Jul 2016 12:36:56 -0400

On Thu, Jul 21, 2016, Stephan Schott wrote:

> I've been doing some simulations using peptides with restraints to maintain
> certain portions of them in close contact (under 15 A). After running some
> steps, the solute drifted away from the center of the box and crossed the
> boundary, point where the restart file was saved. If I try to resume the
> simulations using this restart file, the energy of the system overflows. It
> seems like pmemd.cuda is calculating the distance before reimaging the
> peptides into the PBC and for what I understand the energy overflow might
> be because of the initial force applied to the restraints.

It's hard to know exactly what is going on from this brief description, but
be sure that iwrap=0 in your simulation -- in this circumstance, you don't
want any imaging.

> First steps after restart:
> 0 87.699 13.441
> 5000 ********* *********

Well, for sure, try a run with a much smaller ntpr: you want to find out
what is going on in between step 0 and 5000.
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000

It's odd that the restaint energies are all zero; might be OK, but worth


AMBER mailing list
Received on Fri Jul 22 2016 - 10:00:02 PDT
Custom Search