US in PLUMED + GROMACS ............force constant unit

[tarak karmakar]

Dear All,

In GROMACS 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
[http://www.sciencedirect.com/science/article/pii/S0009261408007975]
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. 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

[Davide Provasi]

Tarak-
the angle collective variable is in radians, so you should use
those units in your input file, and use a kappa of ~500
if you want the forces to be the ones described in the paper.

--
Tarak

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--
Davide Provasi
Dept. of Structural and Chemical Biology
Mount Sinai School of Medicine
Icahn Medical Institute Building
1425 Madison Avenue, Box 1677
New York, NY 10029-6574
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[tarak karmakar]

Thanks a lot for the reply.....:

Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809