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 Emily On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis <emilymariecur...@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 > > Emily > > On Wed, Sep 8, 2010 at 4:05 PM, Justin A. Lemkul <jalem...@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 | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >
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