[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS
jalemkul at vt.edu
Wed May 31 13:52:03 CEST 2017
On 5/31/17 7:06 AM, Tomasz Piskorz wrote:
> Dear all,
> I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen
> that the topology is already available in CHARMM-DrudeFF and I would like
> to transfer it to GROMACS. However, I don't know how to calculate the
> charge of Drude particle, which is required by topology in GROMACS. Does
> anyone know how to do it?
> Atomic polarizability can be described by equation:
> alpha = (q_D)^2/k,
> where k = 418400 kJ/(mol*nm^2) and alpha is given in CHARMM topology (i.g.
> for O in glycine alpha=0.000651 nm^3). However, when I try to calculate the
> charge I always get a wrong result. Is this question which I should use or
> there is something more which I don't take under consideration?
Yes, there is an implicit conversion factor of Coulomb's constant.
qD = sqrt((alpha/kD)/CCELEC)
In CHARMM units, this is
qD = sqrt((0.651/1000)/332.0716)
I'll add the model compounds to the next release of the GROMACS-formatted Drude
force field. I have other issues to sort out before doing that, though.
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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