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
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Jan 18 2012 - 14:30:02 PST
