[gmx-users] about Rg

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 3 21:14:53 CEST 2010

Moeed wrote:
> Hello,
> I am calculating Rg for a system having 8 polymer chains. System is 
> copmressed in 10 ps to the final system size. Rg without nmol option 
> varies between 13 to 2 nm (0 to 10ps ) and remains constant over the 
> whole simulation. Rg with -nmol 8 gives values between 4 to 1.5 nm. nmol 
> is said gives Rg for nmol number of molecules to be analyzed. What does 
> Rg refer to if command is used without nmol?

Using your entire command line would be useful, rather than having to assume the 
commands you used (several of which include -nmol).  Assuming you're using 
g_gyrate, the default is -nmol 1, so any species that corresponds to your 
polymer is likely to be analyzed and assumed to be a single molecule.

You're better off using g_polystat.  It's specifically designed for polymer 
analysis, whereas g_gyrate likely was designed around proteins.


> I dont realize why results are different and why they demonstrate.
> Thanks for your comments
> moeed


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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