On Friday 22 June 2007 10:59, Bert de Groot 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. > > right. one way to include water and still have a manageable system size is > to work with a small droplet of explicit water. > > > Bert
The hessian is the second (numerical) derivative of the atoms in the three dimensions. In the future, I want to calculate the hessian of molecules next to proteins, so the "small droplet of explicit water" will not work here. I do not understand, why I need to calculate the second derivatives of the atoms of the whole system, if I just need it of a small molecule. 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