Re: [AMBER] global scaling of vdW

From: David A Case <>
Date: Thu, 5 Jul 2018 08:35:59 -0400

On Tue, Jul 03, 2018, Korey M Reid wrote:
> I am interested in scaling all vdW interactions and am looking for the
> most appropriate method to accomplish my task. My preference would be
> to scale using epsilon, however, my attempts at doing this from within
> python has failed, here is some sample code:
> Import parmed as pmd
> prmtop=pmd.load_file('prmtop')
> for a in prmtop.atoms:
> a.epsilon=1.1*a.epsilon

Not sure why the above fails.

> I have also attempted a few things within parmed but this option only
> seems to allow editing one by one and modifying 20k+ atoms seems
> tedious.

Using the changeLJSingleType command would involve "only" ntypes commands, one
for each LJ type.

> Lastly, I am currently editing the LENNARD_JONES_ACOEF and
> LENNARD_JONES_BCOEF by hand scaling all values by 1.1, but, again
> this seems to me not the standard method of accomplishing this.

Seems fine to me, and is probably what I would do if I couldn't get parmed to
work as in your top example. The fact that it is "not the standard method" is
not such a persuasive argument.

....good luck....dac

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Received on Thu Jul 05 2018 - 06:00:03 PDT
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