Well, the potential is of the form V=k(x1-x2)^2, but I don't see how it's harmonic. What you would want is the x1 and x2 to refer to dihedral angles. However, the potential in equation 4.70 has this weird phi-phi_0 MOD 2pi term and this delta_phi parameter. It's just not obvious to me how equation 4.70 can be expanded or rearranged to look like a harmonic potential in the dihedral angles. Am I just not seeing something correctly? Bob
On Mon, Feb 25, 2008 at 2:47 PM, David Mobley <[EMAIL PROTECTED]> wrote: > 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 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 > > > _______________________________________________ > 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 > _______________________________________________ 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