From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Mar 03 2014 - 13:01:10 CST
Unless you're using some aggressive enhanced sampling method, this kind of
flip is not supposed to happen often enough to be a problem. Except for
proline, where it is physical. So if you get unexpected rates of amide
inversion, something might have gone wrong during system preparation,
which would need to be fixed before anything else.
Then, to answer your question, it is strongly recommended to leave the
force field files alone (even more so if you made a modification and it
doesn't have the effect you expected). Better would be to apply an extra
restraint or constraint. I'm not an NAMD expert but I'm sure it's
documented somewhere how to do so.
By the way, the CHARMM36 force field is a significant improvement over
On 03/03/2014 01:10 PM, Alex Utev (CMP) wrote:
> I was wondering if there was a way of disallowing omega torsions to flip from trans to cis conformation?
> I have tried removing the corresponding line from the CHARMM parameter file (all22) but this seems to have no effect?
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