[gmx-users] How to implement dihedral restraints
rsugitani at ucdavis.edu
Wed Jan 24 05:48:49 CET 2007
Thanks for your reply,
The test I ran was just rotating a side chain of an amino acid residue
over one of its dihedral angle 360 degrees with dihre_fc = 8000.
I originally thought fc = 8000kJ/mol unit^2 would give fluctuation of
about the half the unit size since I use fc = 8000kJ/mol nm^2 for 0.5A spacing.
But, after I thought twice about it, it would be fc = 80kJ/moml nm^2, for 0.5nm spacing...
So, after I realized that, kJ/mol rad^2 made sense to me and my test run's fluctuation
(about several degress = 1/20 rad = about 3 degrees)
I think Chris meant "my test run" :)
It's good to hear that your implementation can produce a reasonable PMF profile.
I hope mine will, too.
On Tue, 23 Jan 2007 18:26:59 -0500, Chris Neale 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.
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