[gmx-users] Difference in alpha and thole terms for drudeFF

[Justin Lemkul]

On 5/10/17 1:25 PM, Dayhoff, Guy wrote:
> Justin,
>
>    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.
>
> e.g.
> 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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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