Oh yes, the -rdf option! And the run input file! That makes me feel kinda stupid... Thank you very much & sorry for the dumb questions.<br><br>But still, having read the help again, I don't quite get the logic behind g_rdf -com -rdf atom -n -s giving me an all-zero output for the RDF between the COM of the molecule and water oxygen (which is I suppose what I request it to produce). However, using -rdf mol_com seems to work fine.
<br><br><div><span class="gmail_quote">2008/1/11, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Vasilii Artyukhov wrote:<br>> Hi everybody,<br>><br>> I'm dealing with aqueous solutions of some small molecules. Just to clarify:<br>><br>> 1) When I type g_rdf, is the -com option on by default? g_rdf -h makes
<br>> me suspect it is...<br>read again.<br><br>> 2) When I type g_rdf -nocom, what point of the molecule does the<br>> resulting RDF correspond to?<br>it works between atoms unless you use one of the other options.
<br><br>> 3) g_rdf -h says that the -com option makes it calculate the RDF w.r.t.<br>> the COM of the 1st molecule. What about the other one, how is it treated?<br>><br>have you tried it out at all?<br><br> From g_rdf -h:
<br>The option -rdf sets the type of rdf to be computed. Default is for<br>atoms or particles, but one can also select center of mass or geometry<br>of molecules or residues. In all cases only the atoms in the index<br>groups are taken into account. For molecules and/or the center of mass
<br>option a run input file is required. Other weighting than COM or COG can<br>currently only be achieved by providing a run input file with different<br>masses. Option -com also works in conjunction with -rdf.<br><br>> Thanks in advance,
<br>> Vasilii<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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