Thank you Jason!
I'll reduce the ntrelax back to 100 as per your recommendations and the
tutorial. I'll use my input script with the following parameters for
explicit 100 ns CpHREMD production runs then.
REM for CpH
&cntrl
nstlim=100, // No benefit gained from increasing numexchg=500000,
icnstph=2, // For explicit solvent CpH
ntcnstph=100, // Number of steps between attempted protonation state
changes
ntrelax=100, // Number of steps of relaxation dynamics solvph=5.5,
saltcon=0.1, // Same as reference
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
On Tue, Jan 17, 2017 at 10:30 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sun, Jan 15, 2017 at 4:39 AM, Andrew Schaub <aschaub.uci.edu> wrote:
>
> > 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
>
>
> ​Attempting exchanges less frequently will probably improve things a little
> in explicit. But the more frequently you exchange, the better your
> sampling will be. Attempting replica exchanges every 200 fs is probably a
> decent compromise.
>
> For implicit solvent CpHMD, the more residues you have, the more often you
> need to try to exchange (since each protonation state change attempt
> involves one or two neighboring residues only). For explicit solvent,
> replica exchange attempts become more expensive because it attempts *each*
> residue in random order. You might be able to increase this to 200 as well
> to speed up the simulation a little bit, but it will come at a cost of
> reduced protonation state sampling.
>
> The choices for the ntcnstph parameter differ greatly between implicit and
> explicit solvent due to the way that proton exchange attempts are handled.
> nstlim vs. numexchg behaves similarly in both situations. Outside of
> possibly increased simulation efficiency (more pronounced for explicit
> solvent, but probably minimal for both), there is no benefit to using a
> larger value of nstlim.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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>
--
Andrew Schaub
Graduate Program in Chemical & Structural Biology
Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
Luo Lab, http://rayl0.bio.uci.edu/html/
University of California, Irvine
Irvine, CA 92697-2280
949-824-8829 (lab)
949-877-9380 (cell)
aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
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Received on Mon Jan 16 2017 - 18:00:03 PST
