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 <jalem...@vt.edu
<mailto: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 <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
========================================
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