On Fri, May 16, 2014, Valentina Romano wrote:
> Please find in attachment the files you need.
It looks like you have dihedral angle force constants of 5000 or so (!) These
are 2-3 orders of magnitude too big, and you will never be able to do
molecular dynamics with such large forces.
I think that in the past you seemed very worried about having non-planar
groups, but I don't remember ever getting a clear answer to the question of
whether you were seeing *small* or *large* deviations from planarity.
In any event, go back to what Amber or gaff suggest for the magnitudes of
these terms. They have been calibrated against vibrational frequencies of the
out-of-plane modes. It is possible that minor adjustments might be needed (the
original values were determined 30 years ago), but such changes would almost
certainly be minor ones.
....dac
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Received on Fri May 16 2014 - 18:00:02 PDT
