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
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