[gmx-users] Problem with g_rdf

Thomas Schlesier schlesi at uni-mainz.de
Wed Feb 20 14:08:11 CET 2013

My understanding is the following:
If you performed a simulation and then analyse it with different values 
for 'nrexcl' the results will differ since a different amount of 
interactions are excluded. It seems that the exclusion only helps for 
'-rdf atom' and not for '-rdf mol_com'.
But the underlying simulation is the same (you got the output with a 
unique input), only the way you analyse the results changes...

If you change the *.tpr (change 'nrexcl') and run a new simulation, you 
would get complete different results, i.e. the underlying simulations 
changes, due to the fact that you excluded some interactions. More 
important, the results are wrong (from a force field perspective). If 
you turn for a protein 'nrexcl' so high, that the intramolecular 
non-bonded interaction don't get calculated, the protein might unfold 
really fast, since there are no more hydrogen bonds etc...
Think there are some special cases, where one is interested in turning 
of these interactions, but in most cases the resulting trajectory would 
be for the trash bin.


> 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
>>> input
>>> to g_rdf.
>>> -Justin

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