Thanks, Prof. Roitberg. That makes sense. I appreciated it.
Victor
On Wed, Jan 18, 2012 at 4:22 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Dear Victor.
>
> First, just because you did not run shake ON, it does not mean that
> amber does not have it ON as default ! You should look in the manual,
> but more importantly, look at the output file, where the value of ALL
> variables used is listed, including those that you did not set yourself.
>
> Second, there is a strong reason why implicit solvent simulations are
> sometimes slower than explicit ones. Explicit solvent simulations only
> have a short cutoff for the direct non-bonded interactions, while the
> rest is done if fourier space. Implicit solvent simulations need to
> compute all non-bonded pairs. Hence, for small systems, implicit is
> faster than explicit, but for a system like yours, explicit actually wins.
>
> Now, this is in nanoseconds/day. What you need to realize is that in
> THAT time scale, the atoms move 'less' in explicit due to the solvent
> friction, so you might very well be seeing the same level of movement in
> implicit as in explicit, at shorter time scales.
>
> This is of course not very quantitative, and care is required before
> comparisons are done.
>
> Cheers
> Adrian
>
>
>
> On 1/18/12 5:11 PM, Victor Ma wrote:
> > 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
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
> _______________________________________________
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Received on Wed Jan 18 2012 - 15:00:03 PST
