AMBER Archive (2007)

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

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Thu May 31 2007 - 15:18:09 CDT

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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