[gmx-users] Re: Strange form of RDF curve

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 01:40:56 CET 2012

On 11/19/12 11:50 AM, shch406 wrote:
>> I would have chosen the groups in the opposite manner.  You're interested in
> the
>> presence of water around the chosen arginine residue, not the presence of
>> arginine around water, right?  Given this order of chosen groups, the RDF
> seems
>> to make sense (very low probability that arginine is close to all water
>> molecules), though it doesn't represent what you likely want.
>> -Justin
> Of coarse, I'm interested in the presence of water around the arginine.
> But I did reverse order of groups, i.e. I toke water as the "1 group" and
> arginine sige
> chain tip as the "reference group", however have obtained absolutely the
> same curve.
> May be there exist some peculiarity in using g_rdf dialog to select groups?

I've never had an issue with similar commands.  Can you provide us with your 
full g_rdf command line?  Have you verified that the index group for the 
arginine residue is correct?  Can you provide a link to an image of the 
resulting RDF?



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


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