AMBER: cutoff & speed-up of GBSA

From: Wei Chen <>
Date: Wed, 30 May 2007 16:27:53 -0400

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
    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,
    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
RES 1 1642


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 - 06:07:14 PDT
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