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

[Justin Lemkul]

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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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