Thanks Chris. I presume g_sdf won't be helpful for my system. > I think that you have a misconception about what g_spatial does. For a > system with many type A and many type B, you need to average over all > of one type as the central solute to compute an rdf, and perhaps that > is what you want for your sdf. g_spatial, however, does not do any > fitting. g_sdf did that. You can obtain an old version of the source > (4.0.7 should have it I think) if you want to use g_sdf. I have never > used g_sdf myself. > > In case that doesn't answer your question, then let me make one more > point: > > g_spatial requires that a bin exists for every count. Thus either (a) > find a large memory node somewhere or (b) pre-process your trajectory > using trjorder to order the solvent molecules and then keep only the N > closest, then run g_spatial. But again, I think that this will not > provide what you are looking for but is likely to give you a smear > over your box. > > Chris. > > -- original message -- > > Dear all, > > I'm working with a binary solvent mixture containing 2000 molecules > (1800 > type-A + 200 type-B). Both the types of solvent molecules have similar > structure (they are both diatomic molecules) except the polarity.I'm > trying to calculate sdf of type-B solvent molecules. I followed the > step-by-step instructions from the manual using g_spatial. > I'm trying to reduce the bin width to 0.05A. The *.cube file generated > with a bin width of 0.09A is already 4.9GB in size. As I'm more > interested in the first solvation shell around the type-B solvent > molecule, I was wondering if I could find a way to control the maximum > radius of the sphere around central molecule (center of coordinates?)? > Also, can anyone please let me know how g_spatial deals with the angular > part of sdf? > > (I've searched a lot but could not gather enough meaningful information) > > regards, > Debasmita > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > >
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