[gmx-users] Re:Problem with g_rdf

Ali Alizadeh ali.alizadehmojarad at gmail.com
Wed Feb 20 07:58:18 CET 2013

Dear Thomas

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
want) AND
 > 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
individual and
 > average over all. Would require some scripting :( so any better
solutions are
 > welcome.

>>Create a topology with a value of nrexcl sufficient to exclude all
>>intramolecular interactions and create a .tpr file from it.  Use that as
>>to g_rdf.



Ali Alizadeh

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