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
--
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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