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

[Christian Bope Domilongo]

Thank you justin for reply. I have read and follow the second paragraph and
use this command

*g_polystat  -s tmp.tpr -f tmp.xtc -n index.ndx -p persist.xvg*





On 30 January 2015 at 19:14, Justin Lemkul <jalemkul at vt.edu> wrote:

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