Re: [AMBER] Manually extending the size of the virtual box

From: David A Case <>
Date: Mon, 16 Dec 2013 07:30:00 -0500

On Mon, Dec 16, 2013, Eugene Yedvabny wrote:
> I am running gas-phase NVE simulations of a short peptide covered with a
> single or double shell of solvent. The purpose of these simulations is to
> observe desolvation of a peptide as it [hypothetically] transitions from
> bulk-solvent to gas phase, akin to IM-MS.
> Since these simulations are gas-phase with no PBE, I expect the solvent
> molecules to fly off. This, however, breaks the Sander protocol as soon as
> a water molecule goes beyond the simulation virtual box, with the error:
> "The system has extended beyond the extent of the virtual box."

Use igb=6 for simulations like these: this will run a gas-phase simulation,
but does not invoke a virtual box.

...good luck...dac

AMBER mailing list
Received on Mon Dec 16 2013 - 05:00:02 PST
Custom Search