Hello Sayuri,
Yes, you can perform T-REMD with CpHMD turned on. If you want to perform any analysis on the protonation states per temperature, you will need to reorder your CPOUT files after the simulation is completed using the tool fixremdcouts.py (this is available since Amber18). It is important to keep in mind the following: as the reference energies necessary in CpHMD were obtained at 300 K, in principle you should not be using the same reference energy at, for example, 900 K. However, T-REMD will enhance the sampling of your results at 300 K, where the protonation states can be correctly evaluated.
I suggest you to double check for your system if 100 K is a good temperature spacing between neighboring replicas by using the following calculator: http://folding.bmc.uu.se/remd/
I hope this helps,
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: Pacheco, Sayuri <sayuri.pacheco.987.my.csun.edu>
Sent: Friday, May 3, 2019 2:48 PM
To: AMBER Mailing List
Subject: [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD
Hello,
I want to set up a set of temperature replica simulations at pH 1.0 and a
separate set of temperature replica simulations at pH7.0. For example, at
pH 1.0 I would like to run replicas from 100K to 900K at 100K increments
and I would like to use the same temperatures at pH7.0. Is it possible to
have constant pH on while performing TREMD?
Thank you for your help,
*Sayuri Pacheco*
B.S Biochemistry
California State University Northridge, 2018
Research Scholar at the University of Pittsburgh
*sap179.pitt.edu <sap179.pitt.edu>*
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Received on Fri May 03 2019 - 12:30:02 PDT
