Thank you for the help!
Sasha Perkins
Master's Candidate, Penn State University
BSc 2011, University of Florida
On Sun, Nov 27, 2011 at 5:16 AM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Nov 26, 2011, at 5:40 PM, Sasha Perkins wrote:
>
> > Hello,
> >
> > I am a new Amber user and I was wondering if it's at all possible to
> reduce
> > computation time by changing the nrespa variable (or some form of
> multiple
> > time stepping) when running an MD production run of 4ns with constant
> > pressure using periodic boundary conditions of 600 small molecules using
> > Amber 11. My input file looks as follows, however, when using sander it
> > tells me nrespa must be 1 if ntp>0. However, using nrespa=1 will not help
> > me further reduce computation time. Is nrespa>1 only used with NVT or no
> > periodic boundary conditions?
> >
> > &cntrl
> > imin = 0, irest=1, ntx=5,
> > ntb=2, ntp=1, taup=1.0,
> > pres0= 1.0,
> > ig=-1
> > cut = 20.0,
>
> In addition to what Bill said about the multiple image issue, cut==20
> vastly increases the computational cost of a PME calculation by driving up
> the cost of the direct space calculation (which is already typically the
> most expensive part of a PME calculation even at a cutoff of 8Å in my
> experience).
>
> You can safely remove this variable and leave it at the default of 8Å,
> which will make negligible difference to the VDW calculation (since those
> fall off as 1/r^6). This should significantly increase your computation
> time.
>
> Furthermore, I don't see any variable that you've set in your input file
> that doesn't work for pmemd, which is significantly faster than sander for
> any functionality that they both share. Thus, you will see a *significant*
> speedup over your current simulation by reducing cut to 8 and switching to
> pmemd instead of sander (the results are exactly the same for the same
> input between the two programs) without significantly changing the results
> of your simulation.
>
> To answer your original question, though, nrespa > 1 with constant
> pressure simulations (and minimizations) is disabled in both sander and
> pmemd, so in order to get nrespa > 1 working, you'll need to switch to NVT
> or some implicit solvent simulation.
>
> > ntc=2, ntf=2,
> > temp0=300.0,
> > ntt=3, gamma_ln=5,
> > nstlim= 2000000, dt =0.002,
> > ntpr=100, ntwx= 100, ntwr = 1000,
> > nrespa=2
> > &end
>
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
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Received on Sun Nov 27 2011 - 09:00:02 PST
