Re: [AMBER] Applying change to van der Waals for specific pairs of atom

From: David A Case <>
Date: Thu, 20 May 2021 09:08:06 -0400

On Tue, May 18, 2021, Smith, Richard wrote:
>    I am trying to change the weight on the vdW terms (RSTAR and VDW)
>for a particular set of residues to try and keep them apart in the
>simulation.  However, I can't find in the manual how to define these
>residues.  The weight namelist I am using is below, but it appiies it
>to the whole system.  Is there a mask that will allow me to identify
>these residues?

No: these weight-change variables apply to all vdW interactions.

If there are not too many atoms involved, you might be able to get by with
using the changeLJPair action in parmed. But may well be looking at create
some bespoke code to modify the prmtop file in a specific fashion, to get
the behavior you want.


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Received on Thu May 20 2021 - 06:30:02 PDT
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