On Tuesday 07 November 2006 08:46, David van der Spoel wrote: > Tsjerk Wassenaar wrote: > > Hi Alex, > > > > I think you're best off describing the wall with particles. You can > > freeze them to a specific position (make it a freeze-group) and set > > all interactions between them to zero. You can tune your particles to > > be hydrophilic or hydrophobic. > > > > Hope it helps, > > If that really is not what you want, then please write down some > equations how you would treat a hydrophilic wall. Just a Lennard Jones > is not very complicated, and we have actually done something like that > in the past (Wensink et al. Langmuir 16 (2000), p. 7392). I need Lennard-Jones interactions in Z direction between walls and Oxygens of water molecules. And second, repulsion function (also in Z direction) between atoms of peptides and walls. I think that it is possible to introduce periodic boundary conditions only in x and y directions? -- Alex Krukau Physical Chemistry II a University Dortmund tel: + 49 231 755 3938 fax: + 49 231 755 3937 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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