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
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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
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