Re: [AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary?

From: Carlos Simmerling <>
Date: Thu, 12 Mar 2020 07:21:40 -0400

Why not just disable wrapping in the mdin file? Iwrap =0

On Thu, Mar 12, 2020, 7:16 AM Homeo Morphism <>

> I'm modelling interactions of a ligand with a GPCR-receptor under ligand's
> free diffusion. Receptor is membrane-bound. And the ligand is initially
> placed in the solvent on the extracellular side of the receptor.
> Naturally, in some simulations the ligand crosses the periodic boundary
> that separates extracellular part of the receptor from the intracellular
> one and starts interacting with receptor's intracellular loops.
> I've been dealing with this by introducing an nmr distance restraint that
> kicks in once the ligand is, say, 40 angstroms from the receptor's
> extracellular loops and slightly pushes it toward certain extracellular
> loop's amino acid. I make the force which the ligand is pushed with small
> by setting rk3-parameter equal to 0.5 or 0.1.
> I still believe, however, that this introduces a bias - the ligand is
> pushed, however gently, toward the extracellular loops and a certain amino
> acid in particular. Since the ligand's interactions with extracellular
> loops is exactly what I'm trying to model, I'd like to avoid this push.
> But without this kind of restraints how else would I stop the ligand from
> crossing the periodic boundary and interacting with the intracellular parts
> of the receptor?
> Thanks.
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Received on Thu Mar 12 2020 - 04:30:02 PDT
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