[gmx-users] How to compute persistence length in gromacs

Justin Lemkul jalemkul at vt.edu
Fri Jan 30 12:14:56 CET 2015



On 1/30/15 3:10 AM, Christian Bope Domilongo wrote:
> Hi all,
>
> I used g_polystat command in gromacs to compute persistence length and I
> define atom group in index.ndx file. The result is like
>
>   Average end to end distance: 0.203 (nm)
>
> Average radius of gyration:  0.051 (nm)
>
> Average persistence length:  *2.00 bonds* (? why not in nm?)
>

Have you read the second paragraph of the g_polystat help description?  It 
provides lots of detail on exactly how the persistence length is defined and 
calculated.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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