Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field.
Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, <darre...@ece.ubc.ca> wrote: > > Hi, > I just have a quick question on contraints and restraints. My > understanding is that "constraints" fix the position of an atom in > space and "restraints" restrain the deviation of the atom's position > from its equilibrium point. Is that correct? If so, then I am a little > confused by the purpose of "constraints = all-bonds" or "constraints > = none" in an mdp file, since by selection of a force field, which has > bond/angle/dihedral stretching/bending/torsion constants, we are > specifying the constraints applied to the simulation. So then what is > the purpose of "constraints = all-bonds" and "constraints = none"? > > Thanks. > > Darrell > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
