[gmx-users] g_rdf between bonded and nonbonded groups
emilymariecurtis at gmail.com
Wed Sep 8 23:35:50 CEST 2010
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 was
g_rdf -n index -rdf res_com -s full -surf -o rdf08SEPT10.xvg
On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis <emilymariecurtis at gmail.com>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 was
> using was:
> g_rdf -n index -rdf res_com -s full -surf -o rdf08SEPT10.xvg
> On Wed, Sep 8, 2010 at 4:05 PM, Justin A. Lemkul <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:
>> 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.
>> 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
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