How should I change the input files for minimizing, heating and equilibration?
> Date: Tue, 14 Aug 2012 08:09:23 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] Production md
>
> 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.
>
> ...good luck...dac
>
>
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Received on Thu Aug 16 2012 - 01:00:02 PDT
