[AMBER] CpHREMD (explicit solvent) parameter settings inquiry

From: Andrew Schaub <aschaub.uci.edu>
Date: Sun, 15 Jan 2017 18:39:41 +0900

Good Afternoon,

I am setting up a simulation for constant pH replica exchange MD in
explicit solvent. The two tutorials on Jason's blog are great:

I am trying to set up a constant pH REMD in explicit solvent using the two
tutorials as a guide.

My system is larger than that described in the tutorials. I am studying
conformational changes in a system in the range of pH 5.5 to 9, so I am
doing 8 replicas (pH 5.5 to 8.0, in 0.5 stepsize).
Atom Size: 38986
Protein Residues: 376
Titrable Residues: 50
Waters: 11001

How often should I attempt replica exchange swaps?
How often should I attempt to change protonation states?

The tutorial has replica exchange swaps every 100 steps (200 fs), and
protonation state changes every 5 steps ( 10 fs) in pHREMD and every 100
steps (200 fs) for the explcit. I am looking to speed up the simulation, if

Also, the pH-REMD (implicit) tutorial has exchanges attempted every 100
steps (200 fs) [nstlim=100]. Can I increase these to reduce the amount of
exchanges and the give the overall system longer times to relax?

My current input file for pmemd is as follows:

REM for CpH

Best Regards,

Andrew Schaub
University of California, Irvine
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Received on Sun Jan 15 2017 - 02:00:03 PST
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