Hello Saikat,
Are you interested on:
1) describing some structural property of your system at a single value of pH?
2) describing pKa values or a pH-dependent property (like a conformational change)?
If the answer is 2, you should use pH-REMD instead of T-REMD with CpHMD. Simulations at different pH values are important for proper description of case 2.
I answer below your questions, in case you wanna do T-REMD with CpHMD.
1. Should I use -rem = 1 for my simulations?
Correct.
2. In the remd.groupfile should I specify unique cpout filename for each
replica?
Correct.
3. After the run does the cpout file (e.g remd.cpout.001) contains the
protonation states for lowest temp trajectory? Or do I need to process
cpout files like we process all trajectory files to extract a particular
temp trajectory?
You would need to process the cpout files to sort them by target temperature. In Amber18 this is now trivial to do (a new AmberTool called fixremdcouts.py does it easily for you, but the cpout format for REMD simulations in Amber18 is different than in Amber12). I suppose that for the paper you mentioned the code was modified to print the target temperature to the cpout file so that it could be sorted afterwards. I can't imagine how you can do this with Amber12 without modifying the code.
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: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
Sent: Friday, July 6, 2018 6:52 AM
To: AMBER Mailing List
Subject: [AMBER] Need help regarding CpHMD with T-REMD
Dear AMBER Users,
I am trying to do a constant pH MD combined with T-REMD as described in
here:
"Meng, Y., & Roitberg, A. E. (2010). Constant pH replica exchange molecular
dynamics in biomolecules using a discrete protonation model. *Journal of
chemical theory and computation*, *6*(4), 1401-1412."
I am using Amber12 for the proposed simulation.
While trying to set up the system I am having few doubts. It would be very
very helpful if someone can clear my doubts and point me in the right
direction.
My doubts are:
1. Should I use -rem = 1 for my simulations?
2. In the remd.groupfile should I specify unique cpout filename for each
replica?
3. After the run does the cpout file (e.g remd.cpout.001) contains the
protonation states for lowest temp trajectory? Or do I need to process
cpout files like we process all trajectory files to extract a particular
temp trajectory?
With regards,
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Fri Jul 06 2018 - 08:00:02 PDT
