[gmx-users] Difference in alpha and thole terms for drudeFF
jalemkul at vt.edu
Wed May 10 19:44:23 CEST 2017
On 5/10/17 1:25 PM, Dayhoff, Guy wrote:
> Hope this finds you well.
> Im curious if you could provide some insight regarding the differences i’m seeing in
> the alpha and thole values when comparing the GROMACS port of the drudeFF to
> the charmm version. I don’t see a common ratio coming out when comparing them
> and wasn’t sure exactly the units gromacs is using for these two parameters.
> BGLC in the charmm version shows: alpha = -0.614 & thole = 2.458 for C1
The GROMACS files are based on a previous version of the force field. It is not
current with what is on our group's site, for several reasons:
1. There was a pending overhaul to the DNA force field (published yesterday)
2. Carbohydrates are still in flux and have since changed again (our own
internal files, not public)
3. The Drude DD debugging/rewrite was more important and is unfortunately not
yet done due to a number of factors
> BGLC in the gromacs version shows: alpha = 0.001006 & thole = 0.7480 for C1
These are correct for the Drude-2013 force field; please see the references in
forcefield.doc. The GROMACS port only ever claims to match those references.
The conversion is trivial. There are no modifications to the Thole screening
factor; it is often claimed to be unitless but is actually in Angstrom. To keep
the code simple, I leave those values as they are. Alpha in CHARMM is in A^3,
in GROMACS nm^3, so just divided by 1000.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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