Quoting Robert Johnson <[EMAIL PROTECTED]>: > Not sure if anyone saw this...I had a question about how to include > the dihedral restraints in the topology file. Unfortunately, this info > doesn't seem to be in the manual. There isn't a [ dihedral_restraints > ] section listed in Table 5.4. I presume this section should be > formatted as: > > [ dihedral_restraints ] > i j k l 1 phi_0 k delta_phi
I've never done this before, but I recall a discussion about dihedral restraints not too long ago. There is some detailed information on the Wiki: http://wiki.gromacs.org/index.php/Dihedral_Restraints Maybe it will be of use. -Justin > > Is that correct? > > Thanks, > Bob > > On Tue, Feb 26, 2008 at 11:37 AM, David Mobley <[EMAIL PROTECTED]> wrote: > > Bob, > > > > The other way of putting what Mark said is that phi is only meaningful > > on some range (-pi to pi, or 0 to 2pi, depending on how you define it) > > and so what you require is that the potential be harmonic for the > > region in which phi is meaningful. You don't care what happens outside > > that. Or, in this case, you handle the issue by mapping phi values > > outside the allowed range back into that allowed range. > > > > David > > > > > > On Mon, Feb 25, 2008 at 2:24 PM, Robert Johnson > > > > > > <[EMAIL PROTECTED]> wrote: > > > 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 > > > > > _______________________________________________ > > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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