Well, I was just following the AMBER Tutorial therefore did not turn on
SHAKE for implicit calculation.
I wouldn't say that I have "an unreasonable" small solvent box. The cutoff
for the water box is 10A.
solvateoct complex TIP3PBOX 10.0
I have ~8000 water molecules for ~110 residues which is reasonable. Maybe
it's just that I have a small system.
Victor
On Wed, Jan 18, 2012 at 4:01 PM, Aron Broom <broomsday.gmail.com> wrote:
> I have never done implicit solvent calculations, but I don't understand why
> you can't still apply the SHAKE algorithm to your protein (or whatever no
> water thing you are simulating) and thus have a 2fs timestep? Or if the
> thing you are simulating has no hydrogens, just use a 2fs timestep anyway.
>
> Other than that the only thing I can imagine is the size of your explicit
> solvent box (or whatever shape you had). The implicit solvent calculation
> time will depend on the solvent model and the size of your system (without
> water obviously), whereas the explicit solvent calculation will depend
> largely on how many waters you have. Therefore, if your explicit solvent
> system didn't actually have that many waters (you had an unreasonably small
> solvent box) then it would be extremely fast. Anyway, point being that
> implicit will only be faster than explicit when you are getting to ignore a
> large number of waters. Since I've never run them I can't tell you where
> they cross-over.
>
> ~Aron
>
> On Wed, Jan 18, 2012 at 4:48 PM, Victor Ma <victordsmagift.gmail.com>
> wrote:
>
> > hi all
> >
> > I am doing two calculations using the same structure with explicit and
> > implicit solvent for the same time length (5ns). Surprisingly, the
> implicit
> > calculation is actually twice longer than explicit simply because SHAKE
> is
> > on in explicit calculation thus time step is 2fs while in implicit
> > calculation it is 1fs. The simulation itself seems ok. But I'm worried
> that
> > I might miss something here. People generally say implicit calculations
> are
> > a lot faster.
> >
> > Here are my inputs for the production run:
> > IMPLICIT:
> > &cntrl
> > imin = 0, ntb = 0,
> > igb = 5, ntpr = 5000, ntwx = 2500,
> > ntt = 3, gamma_ln = 1.0,
> > tempi = 300.0, temp0 = 300.0,
> > nstlim = 5000000, dt = 0.001,
> > cut = 12.0,
> > ntr=1,
> > ig=-1,
> > /
> > complex (>10)
> > 8.0
> > RES 1
> > RES 15 16
> > RES 67 68
> > RES 78 79
> > RES 98 99
> > RES 109
> > END
> > END
> >
> > EXPLICIT:
> > &cntrl
> > imin=0,irest=1,ntx=5,
> > nstlim=2500000,dt=0.002,
> > ntc=2,ntf=2,
> > cut=10.0, ntb=2, ntp=1, taup=1.0,
> > ntpr=5000, ntwx=2500,
> > ntt=3, gamma_ln=2.0,
> > ntr=1,
> > temp0=300.0, tempi=300.0, ig=-1
> > /
> > complex (>10)
> > 8.0
> > RES 1
> > RES 15 16
> > RES 67 68
> > RES 78 79
> > RES 98 99
> > RES 109
> > END
> > END
> >
> >
> > Thanks for your input!
> >
> > Victor
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 18 2012 - 14:30:03 PST
