AMBER Archive (2007)

Subject: Re: AMBER: performance with implicit solvent

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jun 15 2007 - 15:17:28 CDT

this is expected.
your cutoff is longer in the GB mdin, and the GB simulations are not
optimized for
cutoff (no pairlist) since you normally don't want to use one.
this has been discussed a lot before, try checking the archives.
GB is known to be slower than explicit solvent for large systems (at least
in a per-step way).
have you tried GB in pmemd? I assume you are running sander but you did not
say.

On 6/15/07, Kijeong Kwac <pine994_at_naver.com> wrote:
>
> Hello,
> I am trying to do MD simulations of a large protein system with amber9.
>
>
> What I would like to ask about is the performace of implicit solvent model
> compared to the explicit solvent.
>
> The solute system has 2067 residues with 32566 atoms. When I did an amber
> run with the implicit solvent (cut = 12.0, igb = 5, gbsa = 1)
>
>
> I got a trajectory of 17000 steps for 24 hours run (24 hrs = 86400 sec)
> using 4 cpus (2.66GHz intel dual core).
>
>
>
> But, I also did the amber run with explicit water (39718 water molecules,
> total 151720 atoms).
> then, I get a trajectory of 50000 steps for 38620.92 sec with the same
> machine.
>
>
>
> Compare the two result:
>
>
>
> Total # of atoms: 32566 (implicit), 151720 (explicit)
>
>
>
> # of steps per hour: 708 (implicit), 4889 (explicit)
>
>
>
> I am wondering why the implicit solvent method take much more time than
> with the explicit water.
> Is this situation normal? Or, could there be something wrong?
>
>
>
>
>
> The following is input for the explicit solvent run:
>
>
> &cntrl
> irest = 0, ntx = 1,
> nstlim = 50000, dt = 0.002, nsnb = 10,
> ntt = 1, tempi = 0.0, temp0 = 298.0,
> cut = 9.0, scee = 1.2,
> ntb = 1,
> ntf = 2, ntc = 2,
> ntwx = 200,
> ntr=1, restraint_wt=10.0,
>
> restraintmask='@1958,4028,6574,8644,11190,13260,15806,17876,20422,22492,25038,27108,29654,31724'<restraintmask=%27_at_1958,4028,6574,8644,11190,13260,15806,17876,20422,22492,25038,27108,29654,31724%27>
> &end
>
>
>
> The following is input for the implicit solvent run:
>
>
> &cntrl
> imin = 0, irest = 0, ntx = 1,
> nstlim = 200000, temp0 = 298.0, dt = 0.001,
> ntwr = 0,
> tempi = 298.0,
> ntt = 3, gamma_ln = 1,
> cut = 12.0, igb = 5, gbsa = 1,
> ntb = 0,
> ntf = 2, ntc = 2,
> ntwx= 250, nscm = 0,
> ntr=1, restraint_wt=10.0,
>
> restraintmask='@1958,4028,6574,8644,11190,13260,15806,17876,20422,22492,25038,27108,29654,31724'<restraintmask=%27_at_1958,4028,6574,8644,11190,13260,15806,17876,20422,22492,25038,27108,29654,31724%27>
> /
>
>
> <http://www.naver.com>NAVER <http://www.naver.com/> Korea's No.1 search
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> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
===================================================================

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