Hi VinÃcius,
Thank you for you prompt reply! I will attempt the simulations and look at
the temperature generator to get a better range of temperatures to use in
the simulations.
Sincerely,
*Sayuri Pacheco*
B.S Biochemistry
California State University Northridge, 2018
Research Scholar at the University of Pittsburgh
*sap179.pitt.edu <sap179.pitt.edu>*
On Fri, May 3, 2019 at 3:15 PM Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:
> 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,
>
>
> VinÃcius 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 - 13:30:02 PDT
