Robert, I am not sure which manual you are looking at, but in the GROMACS 3.3 manual, equation 4.70 gives the dihedral restraint as harmonic.
David On Mon, Feb 25, 2008 at 10:10 AM, Robert Johnson <[EMAIL PROTECTED]> wrote: > Hello everyone, > I am trying to calculate the absolute free energy of binding between a > DNA base and a nanotube. To do this, I am first calculating the free > energy associated with restraining the base in the correct binding > geometry in accordance with Boresch et. al. J. Phs. Chem. B., 107, > 2003. In this paper, all restraints (1 distance, 2 angles, 3 > dihedrals) are assumed to be harmonic. In Gromacs, there already > exists a harmonic distance restraint. Technically, the angle restraint > (Equation 4.67 in the manual) is not harmonic. However, for small > angle displacements it can be approximated as harmonic, so that's not > a problem either. > > However, there is no harmonic dihedral restraint. A reasonable > solution would be to use an improper dihedral (Equation 4. 59 in the > manual) for the restraint. Is this alright, or are there any problems > that could arise from using this? To my knowledge, exclusions are > defined by bonds. Thus, I don't think I have to worry about the > improper dihedral affecting the exclusions. Is this correct? > > Thanks, > Bob > _______________________________________________ > 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 > _______________________________________________ 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
