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

[Justin Lemkul]

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

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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