[gmx-users] g_rdf between bonded and nonbonded groups

[Justin A. Lemkul]

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.

-Justin

> 
> Thank you in advance for any help.
> 
> Emily
> 

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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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