<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Hi Justin,<div><br></div><div>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:</div>
<div><br></div><div><div>g_rdf -n index -rdf res_com -s full -surf -o rdf08SEPT10.xvg</div><div><br></div><div>Emily</div></div><div><br></div></span><br><div class="gmail_quote">On Wed, Sep 8, 2010 at 5:31 PM, Emily Curtis <span dir="ltr"><<a href="mailto:emilymariecurtis@gmail.com">emilymariecurtis@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Justin,<div><br></div><div>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:</div>
<div><br></div><div><div>g_rdf -n index -rdf res_com -s full -surf -o rdf08SEPT10.xvg</div>
<div><br></div><font color="#888888"><div>Emily</div></font><div><div></div><div class="h5"><br><div class="gmail_quote">On Wed, Sep 8, 2010 at 4:05 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
Emily Curtis wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
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:<br>
<br>
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?<br>
<br>
</blockquote>
<br></div>
You set nrexcl in the topology, not directly in the .tpr file.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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:<br>
-surf<br>
</blockquote>
<br></div>
What is your exact command line? Which version of Gromacs are you using? In the latest version I cannot reproduce this error.<br>
<br>
-Justin<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thank you in advance for any help.<br>
<br>
Emily<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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