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 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
