[gmx-users] about Rg

[Justin A. Lemkul]

Moeed wrote:
> Hello Justin,
> 
> Now I am using g_polystat for calculating Rg. However results are pretty 
> similar to those obtained from g_gyrate. The command line I am using is
> 
> g_polystat -f *.trr -s *.tpr -o polystat-mw  -n *.ndx -mw -xvgr -w
> 
> - I noticed -mw option does not change Rg. Also When I choose all chains 
> in index file Rg is exactly the same as choosinfg only the first chain! 
> For other chains Rg is different. Is it possible to get average Rg of 
> all chains? and compare with one single chain?

That's what g_polystat is calculating.  See g_polystat -h.

> -
> - I tried to get persistent length as well but -p option is not working. 
> the output file -p persist.xvg:
> 

Are you choosing an appropriate index group for this calculation?  Again, read 
g_polystat -h for the requirements.

-Justin

> @TYPE xy
>      0.000      nan
>      0.100      nan
>      0.200      nan
>      0.300      nan
>      0.400      nan
>      0.500      nan
>      0.600      nan
>      0.700      nan
>      0.800      nan
>      0.900      nan
> . .
> Thanks,
> moeed
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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