AMBER Archive (2007)

Subject: Re: AMBER: cutoff & speed-up of GBSA

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu May 31 2007 - 15:30:00 CDT

have you tried using pmemd?

On 5/31/07, Wei Chen <cwbluesky_at_gmail.com> wrote:
>
> Dr. Simmerling,
>
> Thanks for your response.
>
> In order to speed up, I have to make cutoff and rgbmax as small as
> possible. From my single point calculation, I see that a 16 Angstrom cutoff
> should be good. But I am not sure whether I have to use a large value for
> rgbmax, since there is a difference of 500 kcal/mol between rgbmax=16 and
> rgbmax=999, which is 1% of total elec. energy. Using large rgbmax really
> slows down the simulation.
>
> Wei Chen
>
>
>
> On 5/30/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> >
> > GBSA is sander is not efficient for large molecules.
> > as has been stated in the past, calculations in explicit water
> > can actually be much faster since you are using a shorter cutoff and
> > because there is a nonbond pairlist.
> >
> > try to use GB in pmemd, that may help with speed.
> >
> >
> > On 5/30/07, Wei Chen <cwbluesky_at_gmail.com> wrote:
> > >
> > > Hello, Amber users,
> > >
> > > I got a big protein that has about 25,000 atoms. I try to run an
> > > implicit MD using GBSA. Because the size of the protein, I have to use a
> > > small cutoff and rgbmax. In order to get an appropriate cutoff and rgbmax, I
> > > calculated a single point energy when varing cutoff and rgbmax, separately.
> > > In the attachment, the first two plots are electrostatic & Vdw energy verse
> > > cutoff when rgbmax was fixed at 16 Angstrom. The third plot is electrostatic
> > > energy verse rgbmax when cutoff was fixed at 16 Angstrom. The electrostatic
> > > energy is the sum of electrostatic energy in vaccum and polar solvation
> > > energy. In the first plot, I see the electrostatic energy converges when
> > > cutoff >= 14 Angstrom. Actually, the electrostatic energy is -
> > > 59497.1116 kcal/mol without cutoff. So it is very close. In the second
> > > plot, Vdw energy has larger variation than elec. energy. I think the Vdw
> > > force should vary slightly considering it is close to isotropic. Am I right?
> > > According to first two plots, a cutoff >= 14 Angstrom should be enough for
> > > my simulation. In the third plot, the elec. energy varies a lot verse
> > > rgbmax. So the elect. energy is much more sensitive to rgbmax. It seems to
> > > me that a rgbmax >= 24 Angstrom should be used ( the elec. energy is -
> > > 58980.5952 kcal/mol with rgbmax=999). Is this reasonable?
> > >
> > > Another problem is with the speed of GBSA. I set cutoff=16 and
> > > rgbmax=16. Control parameters as follows:
> > >
> > >
> > > ----------------------------------------------------------------------------
> > >
> > > cat <<eof > mdin
> > > heat up structure
> > > &cntrl
> > > imin=0,
> > > ntc=2, ntf=2,
> > > cut=16.0, ntb=0, ntr=1,
> > > nstlim=10000, dt=0.002, nrespa=2,
> > > ntt=3, gamma_ln=1.0, tempi=0.0,
> > > igb=2, saltcon= 0.15, gbsa=1,
> > > intdiel=1.0, extdiel=80.0, rgbmax=16.0,
> > > nscm=1000,
> > > ntx=1, irest=0, ntpr=1, ntwx=100, ntwr=100,
> > > ntwv=500, nmropt=1,
> > > /
> > >
> > > #
> > > #heat up algorithm:
> > > #
> > > #from steps 0 to 10000: heat the system from 0K to 300K
> > > #
> > > &wt type='TEMP0', istep1=0,istep2=10000,value1=0.,
> > > value2=300., /
> > >
> > > &wt type='END' /
> > >
> > > keep all atoms restrained
> > > 5.0
> > > RES 1 1642
> > > END
> > >
> > >
> > > --------------------------------------------------------------------------------------
> > >
> > > I used SHAKE and set nrespa=2 in order to speed up. But it was still
> > > very slow. It is about 35 s/step on a single 600MHz R14000 CPU. As a
> > > comparison, I ran an explicit MD in a water box that includes ~200,000
> > > atoms, 8 times bigger. I used Amber force field, but ran it in NAMD with
> > > cutoff=12. This costs ~20 s/step on the same single CPU. I searched on the
> > > mail list. Somebody also found that GBSA was slow for a big molecule. I am
> > > wondering if there is any way to speed it up today.
> > >
> > > I am appreciate for any response.
> > >
> > > Wei Chen
> > >
> > >
> > >
> > >
> >
> >
>

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