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
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