[gmx-users] Re: g_rmsf

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 9 03:57:03 CET 2011

bharat gupta wrote:
> Hi,
> I want to calculate the RMSF of residues and not of protein ... how can 
> this be done with g_rmsf..
> Also I want to see the rmsf of certain residues .. for which I created 
> the .ndx file containint those residues only .. and after using g_rmsf 
> with index file gives the RMSF for whole protein backbone and not for 
> that index file residues ... what shall I do to have RMSF of index file 
> residues ??

The default output of g_rmsf is a plot of RMSF (of each residue) vs. residue. 
No index file is required to obtain this, unless you want to do the fitting to 
some custom group.  Is this not what you want?


> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
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> Pusan National University
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> South Korea
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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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