From: kakali sen (kakalisen_at_gmail.com)
Date: Sun Apr 10 2011 - 12:48:17 CDT
I was performing a 2D ABF for rotation of a glutamate residue along its
CA-CB and CB-CG bond. I had divided the whole scan from -180 to +180 for
both into 4 quadrants and before starting ABF I performed 3ns npt run with
the angles constrained in each of the quadrant. The following observation
is what I don't understand. When I check dcd trajectory from abf run, I
observe that the angles don't stay in the quadrant specified except for the
one which represents the the equilibrium values (i.e. when no constraint or
abf is performed).
I am using onesitesystemforce in my abf moldule.
Besides using upper and lower boundary conditions, I tried to use upperwall
and lowerwall constant abut when I use the later I encounter the following
ERROR: Constraint failure in RATTLE algorithm for atom 3826!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely.
Any suggestion will be very helpful.
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