it looks like you'll want to look at the code and likely modify it,
carefully skipping some of these "sanity" checks. some things in GB may be
hardcoded (bad, I know) to check and make sure that your inputs will work
with a GB model. Unfortunately, these still may be checked when using the
GB routines to do actual gas-phase calculations. You can tell from this
that Amber is really not carefully designed for gas phase simulations - in
fact, one would have to wonder whether using the charge model in our force
fields is appropriate for the kind of process you're trying to simulate...
On Mon, Dec 16, 2013 at 2:03 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>wrote:
> 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 amber.ambermd.org
> Date: December 16, 2013 at 4:30:46 AM
> To: AMBER Mailing List amber.ambermd.org
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 16 2013 - 11:30:04 PST
