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

From: Eugene Yedvabny <>
Date: Mon, 16 Dec 2013 11:03:54 -0800

Hello Dr. Case,

Unfortunately it looks like igb==6 does not support TIP4P-Ew water model. When I try to run my simulation I get the following error:

"Cannot use igb>0 with extra-point force fields"

I was able to run it with TIP3P water model after stripping all the solvent and then solvating a shell of TIP3PBOX in tleap. I would prefer, however, to keep the position of the water molecules as they are in my original pdb, since they are already minimized and equilibrated. If there an easy way to convert one water model to another and still keep the center of the water molecule at the right position?

Thank you,
Eugene Yedvabny
From: David A Case David A Case
Reply: AMBER Mailing List
Date: December 16, 2013 at 4:30:46 AM
To: AMBER Mailing List
Subject:  Re: [AMBER] Manually extending the size of the virtual box
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

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