Hello Kolattukudy,
There are some optional flags in finddgref.py that should help you with that. May you copy the exact command you are using and the output finddgref.py is printing so I can give you a suggestion?
Thanks,
VinÃcius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Jan 20, 2020, at 10:44 AM, Kolattukudy P. Santo <santotheophys.gmail.com<mailto:santotheophys.gmail.com>> wrote:
[External Email]
Hi
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*
*USA*
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Received on Mon Jan 20 2020 - 12:30:01 PST
