Re: [AMBER] Production md

From: David A Case <>
Date: Thu, 16 Aug 2012 08:08:34 -0400

On Thu, Aug 16, 2012, ariana karakutuk wrote:
> How should I change the input files for minimizing, heating and equilibration?

I seem to have not made myself clear in the earlier post (below). The problem
(as I see it) has nothing to do with your input files. Rather, I am
suggesting that you reconsider the choice of trying to carry out GB
calculations with explicit ions.


> > On Tue, Aug 14, 2012, ariana karakutuk wrote:
> > >
> > > We've prepared the missing residues using the
> > > software COOT. During dynamics the protein behaves normally, but the
> > > solvent ions (3 Na+ ions) diffuse very far away from each other.
> >
> > This is probably to be expected. First, it is likely that forces holding any
> > individual sodium ion to its initial postion are very weak, so that they would
> > be expected to move away during dynamics. This is especially true if the
> > sodiums are held in place by the crystal lattice, which is not present (as I
> > understand it) in your simulation.
> >
> > Second, the Amber GB model was never intended to be used with explicit
> > ions, and the parameters have not been optimized for such calculations.
> >

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Received on Thu Aug 16 2012 - 05:30:03 PDT
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