[gmx-users] Re:Problem with g_rdf
ali.alizadehmojarad at gmail.com
Wed Feb 20 07:58:18 CET 2013
I have a question you and Justin,
I had this problem like you, As Justin said you have to exclude all
intermolecular interaction by increasing nrexcl in your topology file,
I have done the step that there is in gromacs manual, My peak values decreased.
But I have a question(Justin and you):
When I change nrexcl in my topology file, I use grompp to create .tpr file,
Then I use this .tpr file to represent rdf(with my prior results),
Now, I like changing the nrexcl in topology for my new simulation,
Does my result change? What is the differences between my first
simulation and second simulation?
On 2/19/13 3:10 PM, Thomas Schlesier wrote:
> Dear all,
> I have a question regarding g_rdf.
> My system consits of 10 disacchardids (in the following A-B, with
> A-ring/monosaccharid and B-ring/monosaccharid) and i want to
determine the RDF
> (with flag '-rdf mol_com')for A-A, B-B and the intermolekular for A-B
> A-A and B-B is no problem.
> But for A-B g_rdf determines the intermolecular contribution (which i
> the intramolekular contribution (which i wanted to be excluded).
> Any (nice) ideas to solve this problem for GMX 4.0.7?
> Long way would be to calculate each intermolecular contribution
> average over all. Would require some scripting :( so any better
>>Create a topology with a value of nrexcl sufficient to exclude all
>>intramolecular interactions and create a .tpr file from it. Use that as
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