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From: Wei Chen <cwbluesky.gmail.com>

Date: Thu, 31 May 2007 16:18:09 -0400

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.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.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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Received on Sun Jun 03 2007 - 06:07:28 PDT

Date: Thu, 31 May 2007 16:18:09 -0400

Dr. Simmerling,

Thanks for your response.

In order to speed up, I have to make cutoff and rgbmax as small as possible.

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.gmail.com> wrote:

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Received on Sun Jun 03 2007 - 06:07:28 PDT

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