Date: Tue, 23 Apr 2019 22:51:31 +0000
Hello Zimin,
Could you please send the prmtop and cein files you mentioned so I can take at look at the discrepancies you are talking about? Also, are you referring to the charges of the HEH residue?
Now answering your last question: once the constant redox potential simulation starts, the charges are overwritten by the set of charges obtained from the cein file. Different redox states have different charge distributions in the cein file.
All the best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Feng, Zimin <Feng.Zimin.hydro.qc.ca>
Sent: Tuesday, April 23, 2019 6:03 PM
To: Cruzeiro,Vinicius Wilian D
Cc: AMBER Mailing List
Subject: charge in constant redox cein file vs. prmtop file
Hi Vinicius or anyone who’s familiar with it,
I noticed that the charges in cein file and the charges in prmtop file don’t really match. This is the case even in the tutorial example.
Is it acceptable? My guess is that prmtop file’s charge is overwritten by cein? Or the charges in cein was used for redox transition only and prmtop charge is used for the rest of the evolution?
Thank you in advance!
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