On Friday 22 June 2007 11:07, Mark Abraham wrote: > David van der Spoel wrote: > > Christian Seifert wrote: > >> Hi. > >> > >> Perhaps, I made a mistake in describing my problem. I can not believe, > >> that no one ever tried this before. > >> > >> I have a phosphate in water and want to calculate the hessian just for > >> the phosphate. How do I do that? > > > > there is a contradiction here in that you say the phosphate is in water > > and you want to do the NMA for just the phosphate. Something like that > > might work with a continuum solvent but I don't know how you would do it > > with explicit solvent. > > Well you could just find the second derivatives of the energy with > respect to the phosphate atomic coordinates numerically... but that > doesn't sound like a good way to get numbers that mean anything. > > Mark
Yes, that is exactly what I want to do. Is there any keyword to calculate the hessian for a group of molecules/ a molecule in a large simulation system? Christian. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
