Re: [AMBER] Production md

From: David A Case <>
Date: Tue, 14 Aug 2012 08:09:23 -0400

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 Tue Aug 14 2012 - 05:30:04 PDT
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