[gmx-users] g_rdf between bonded and nonbonded groups

[Justin A. Lemkul]

Emily Curtis wrote:
> Hi Justin,
> 
> Thank you for your help.  I will edit the topology file.  I am running 
> GROMACS 4.0.7.  I can download the latest version.  The command line I 

There's your problem.  The -surf option only appears as of version 4.5.

> was using was:
> 
> g_rdf -n index -rdf res_com -s full -surf  -o rdf08SEPT10.xvg
> 

As an aside (which you will surely discover by reading g_rdf -h), the -surf
option requires a string after it; it is not a simple boolean.

-Justin

> Emily
> 
> On Wed, Sep 8, 2010 at 4:05 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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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

========================================