[gmx-users] PLUMED-GROMACS force constant, angle unit

[David van der Spoel]

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se