[gmx-users] Re: what is sigma in gromacs? the radius of a sphere or the diameter of a sphere?

Justin Lemkul 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
> angstroms?

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.
Postdoctoral Fellow

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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