[gmx-users] g_rdf between bonded and nonbonded groups

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 8 22:05:50 CEST 2010

Emily Curtis wrote:
> I would like to calculate the inter- and intra-molecular radial 
> distribution functions separately.  I have read through g_rdf -h many 
> times and I have a few questions:
> 1.  I think that I may have to modify a trp file (and not use it for the 
> simulations) by setting the nrexcl to the number of bonds I would like 
> the calculation to exclude.  I cannot figure out where in the tpr file I 
> should add the nrexcl term.  I have tried to sort through the manual to 
> figure out how to make this modification but I cannot figure it out. 
>  Does anyone have any suggestions?

You set nrexcl in the topology, not directly in the .tpr file.

> 2.  In D.56 g_rdf of the Gromacs manual it says that the option -surf 
> can be used along with -rdf to only calculate the rdf of a molecule with 
> its closest neighbor in a set.  Can this option be used for calculating 
> the intramolecular radial distribution function or am I completely 
> misinterpreting the manual?  If it can be used how is this done?  I 
> tried to use it but I get the error message:  Invalid command line argument:
> -surf

What is your exact command line?  Which version of Gromacs are you using?  In 
the latest version I cannot reproduce this error.


> Thank you in advance for any help.
> Emily


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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