Re: [AMBER] using accelerated MD on membrane proteins?

From: Robin Betz <>
Date: Wed, 28 Aug 2019 10:39:36 -0700

I've run aMD on membrane-bound proteins successfully using the tutorial's
suggestion of calculating the boost based on the number of protein
There isn't really a "gold standard" for calculating the boost term, but
when I reviewed the literature it was always in terms of the protein with
varying kcal/mol/residue constant terms.
That makes sense to me, as I want to increase sampling of protein
conformational space by bumping up the dihedral potential energy
proportional to how many dihedrals in the protein there are.
My guess is that adding in the number of lipid residues to the calculation
will yield a boost term that will explode the system.
You might try both ways; it's usually pretty obvious when the boost term is
too high (everything explodes).


On Wed, Aug 28, 2019 at 9:09 AM Homeo Morphism <>

> I'm going through section 20.2.3 of the Amber manual. In there the
> parameters necessary for starting aMD are calculated in terms of the number
> of protein residues. I suspect that protein residues are just sort of a
> placeholder for dihedrals. But what if I have non-protein residue
> dihedrals? Such as lipid dihedrals, for example. How do I account for them?
> Any ideas how aMD parameters should be evaluated in that case? Thank you.
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Received on Wed Aug 28 2019 - 11:00:02 PDT
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