[AMBER] convergence of Ref energies in cpHMD

From: Kolattukudy P. Santo <santotheophys.gmail.com>
Date: Mon, 20 Jan 2020 13:43:20 -0500

I am trying to run cpHMD for a non-standard molecule. I find it hard for
finddgref.py to converge and the fraction of protonation % is very
fluctuating (1 million equillibration steps) . My residue is pretty large
( about 120 atoms ) as it is a side chain of a carbohydrate polymer
Any strategy for fast convergence ?

*Dr. Kolattukudy P.  Santo*
*Post doctoral Associate *
*Department of Chemical and Biochemical Engineering*
*Rutgers, The State University of New Jersey*
*New Brunswick, New jersey*
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Received on Mon Jan 20 2020 - 11:00:02 PST
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