[gmx-users] pair correlation function pbc=0?
spoel at xray.bmc.uu.se
Mon Jun 17 21:22:10 CEST 2002
On Mon, 2002-06-17 at 21:51, Mehmet Suezen wrote:
> David wrote:
> > On Mon, 2002-06-17 at 20:51, Mehmet Suezen wrote:
> > > Dear Gromacs Community,
> > >
> > > Does anybody have an idea that What is the main difference for
> > > the RDF algoritm with and without pbc in gromacs/general? Normalization
> > What do you mean?
> > You need PBC to see interactions between atoms over box boundaries,
> > otherwise the height of the RDF peaks would be too low
> Basically, if I use pbc=0, does gromacs handle rdf algorithm as in pbc?
But this is not an option for g_rdf. g_rdf computes all interactions
with PBC. If you have an isolated system, make sure that your box is
large enough, such that you have a vacuum boundary around it.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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