[gmx-users] How to implement dihedral restraints

[David Mobley]

Chris,

On 1/23/07, Chris Neale <chris.neale at utoronto.ca> wrote:
> Quoting manual-3.3 page 58
> "Note that in the input in topology files, angles are given in degrees
> and force constants in kJ/mol/rad2."
>
> I assume here that force constants refers to dihre_fc. However, although the test
> PMF's that I have generated for the alanine dipeptide have the correct shape, the
> WHAM-PMF magnitudes that are too large by a factor of 10-20.
>
> Please describe the test that you ran.

I am not sure what you mean by "Please describe the test you ran." Who?

Speaking for myself, I compute PMF's for rotating dihedral angles all
the time and my magnitudes are correct, with the units as stated (I
use our own WHAM implementation, so I can't vouch for whatever you're
using). Maybe you can elaborate? (To double-check, the units are
kJ/mol*rad^2.)

Thanks,
David


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