[AMBER] query about scaling of nonbonded interactions.

From: Prof. Mark Wilson via AMBER <amber.ambermd.org>
Date: Fri, 16 Aug 2024 10:10:10 +0100

hI,

I am wanting to setup a hamiltonian replica exchange simulation
where, in successive replicas, the interaction between a polymer and a
surface
are reduced (by reducing the vdw interactions).

I naively thought I would be able to use parmed to do this.
So, for example, I would use lines such as
changeLJPair :98-1297.%h1 :1-97.%ca 1.3870  0.00157

but I think what this does is change all the h1-ca interactions in the
system
not the ones between the surface (residues 98-1297) and polymer
(residues 1-97);
and in addition alters 1-4 interactions

my question is essentially, is there another way to do this
so that I can have simulations in which the interaction is weakened
(this is to improve exploration of the surface by the polymer)

Mark

-- 
Prof. Mark R. Wilson
Department of Chemistry
University of Durham
South Road
Durham
DH1 3LE
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Received on Fri Aug 16 2024 - 02:30:01 PDT