[AMBER] Manually extending the size of the virtual box

From: Eugene Yedvabny <eyedvabny.berkeley.edu>
Date: Mon, 16 Dec 2013 01:19:44 -0800

Hi Amber community,

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."

I tried to expand the box with 'set peptide box 300' in tleap, but that
doesn't seem to do anything since I am not using periodic bounds. Is there
a way to manually expand the virtual box so that I can simulate for a
longer period of time without having to constantly restart the simulation?

Thank you,
Eugene Yedvabny
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Received on Mon Dec 16 2013 - 01:30:04 PST
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