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:
http://jswails.wikidot.com/ph-remd
http://jswails.wikidot.com/explicit-solvent-constant-ph-md
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
possible.
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
&cntrl
nstlim=100,
numexchg=500000,
icnstph=2,
ntcnstph=100,
ntrelax=200,
solvph=5.5,
saltcon=0.1,
tempi=300,
temp0=300,
ntc=2,
ntf=2,
dt=0.002,
ntt=3,
ntpr=5000,
ntwx=5000,
ntwr=250000,
cut=8,
imin=0,
ntx=5,
irest=1,
ntxo=2,
ig=-1,
ioutfm=1,
iwrap=1,
gamma_ln=5.0,
/
Best Regards,
Andrew Schaub
University of California, Irvine
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Received on Sun Jan 15 2017 - 02:00:03 PST
