[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?
jalemkul at vt.edu
Thu Aug 15 14:32:04 CEST 2013
On 8/15/13 8:28 AM, grita wrote:
> Hi Justin,
> Wikipedia says: "sigma is the finite distance at which the inter-particle
> potential is zero"
> But if I want to simulate particles with a certain diameter, where can I set
> the diameter in Gromcas?.
> For example, a sphere with a diameter of 5 angstroms, would then sigma 5
No. There are no explicit settings for particle size anywhere in Gromacs (with
the possible exception of vdwradii.dat, but that's only used by genbox and
g_sas). Dynamics rely on inter-particle potentials. You would have to derive
and/or tune parameters that represent physical reality of what a particle's size
should be such that it is reflected in the outcome of MD.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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