[gmx-users] g_rdf

[Rama Gullapalli]

Dear Dr Spoel
  Thanks for the prompt reply. Yes I did shuffle the trajectories. I shall try to recompute after deshuffling the trajectories.
  Thanks again,
  Sincerely
  Regards
  Rama

David van der Spoel <spoel at xray.bmc.uu.se> wrote:  Rama Gullapalli wrote:
> Hi GMX ers,
> I posted this question earlier, but did not receive a reply. Hope to get 
> an answer this time around.
> 
> I was wondering what could be the origin of a spike at close distances 
> when I compute the RDF of  N-P atoms  in a lipid bilayer system (<0.25 
> nm) I tried using -cut option and also increasing the nrexcl to 5 in the 
> N and P atoms ( to avoid intramolecular contributions?)
> And yet, I still get that spike.

maybe your index file is incorrect, or the trajectory does not match the 
tpr (did you use shuffling?)

> Any insight would be very helpful
> Thanks
> Rama
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,   75124 Uppsala, Sweden
phone: 46 18 471 4205  fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org   http://folding.bmc.uu.se
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