Vasilii Artyukhov wrote:
Hi everybody,
I'm dealing with aqueous solutions of some small molecules. Just to clarify:
1) When I type g_rdf, is the -com option on by default? g_rdf -h makes
me suspect it is...
read again.
2) When I type g_rdf -nocom, what point of the molecule does the
resulting RDF correspond to?
it works between atoms unless you use one of the other options.
3) g_rdf -h says that the -com option makes it calculate the RDF w.r.t.
the COM of the 1st molecule. What about the other one, how is it treated?
have you tried it out at all?
From g_rdf -h:
The option -rdf sets the type of rdf to be computed. Default is for
atoms or particles, but one can also select center of mass or geometry
of molecules or residues. In all cases only the atoms in the index
groups are taken into account. For molecules and/or the center of mass
option a run input file is required. Other weighting than COM or COG can
currently only be achieved by providing a run input file with different
masses. Option -com also works in conjunction with -rdf.
Thanks in advance,
Vasilii
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