Thanks Justin! Can you also comment on the other issue, the lack of smoothness? I guess this is because I don't have that many individual coms per bin to accurately compute the rdf? At least I think that makes sense since when I increase the value of -bin in gmx rdf I get an increase in "smoothness" and fewer "jump" back and forth.
Den mån 20 jan. 2020 kl 15:50 skrev Justin Lemkul <jalem...@vt.edu>: > > > On 1/20/20 9:48 AM, Gmx QA wrote: > > Hi list, > > > > I am working on a system that contains lipids, but since there is no > water > > present they do not form a typical bilayer. > > > > In these systems I also have some smaller drug-like molecules. What would > > be the best way to get a proper rdf-function between the lipids and the > > drugs? Since both types of molecules are larger than single atoms, I > tried > > to calculate a com-com rdf using > > > > -selrpos whole_mol_com -seltype whole_mol_com > > > > but the resulting curve is very rugged (i.e. not as smooth as > > the atom-rdf's typically shown). The minimum distance (the distance > > below which the pdf is zero) also appears to be quite small, since one > the > > molecules is a lipid I would have expected a larger distance than > > the corresponding value seen in e.g. an oxygen-oxygen rdf for water. > > > > Might all of this be consequences of the fact that I have a com-com rdf > > between a limited number of molecules? > > Yes, likely. You could in principle have a COM-COM RDF value very close > to r=0 if a lipid were to wrap around a drug molecule, so I don't think > any of your results are unexpected. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.