Hi David, Thanks for the reply. But I rechecked the paper [ http://www.sciencedirect.com/science/article/pii/S0009261408007975] as I mentioned earlier, the unit of the harmonic force constant for the dihedral is kcal/mol/deg^2. Again if the force constant unit is independent of degree or radian then why should I multiply by the factor 180/pi ? Can you please make it clear, I gotta confused. Thanks,
Tarak On Tue, Aug 14, 2012 at 7:17 PM, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 2012-08-14 14:27, tarak karmakar wrote: >> >> Dear All, >> >> In the manual I see the unit of the k{theta} is kJ/mol/rad^2. But >> Neale et al in Chemical Physics Letters 460 (2008) 375–381 has applied >> the harmonic restraints with a force constant of >> 0.0364 kcal/mol/deg^2 for the phi and psi dihedral angle of alanine >> dipeptide. If I convert it into KJ/mol/rad^2 then its coming out to be >> around 500.4 KJ/mol/rad^2. > > For dihedrals the unit is kJ/mol not kJ/mol/rad^2 (except impropers). > Therefore multiply by 180/Pi once gives approx 2 kJ/mol. > If you indeed want to apply restraints then this may be reasonable, but do > check your time steps. > >> >> Can I safely use this large force constant value to do US for the same >> system? >> I am utilizing the PLUMED software patched with gromacs. Should I >> specify the angle in degree unit in plumed input file, since in >> GROMACS ffbonded.itp file angles are defined in degree unit ? >> Thanks >> >> Tarak >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists