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 - 04:00:02 PDT
