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 ______________________________________ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot _______________________________________________ gmx-users mailing list [email protected] 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
