Re: [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 <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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