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? 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 Thank you in advance for any help. Emily
-- 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
