AMBER Archive (2002)

Subject: gB vs. explicit (fwd)

From: amber_at_heimdal.compchem.ucsf.edu
Date: Tue Dec 03 2002 - 16:57:53 CST

---------- Forwarded message ----------
Date: Tue, 3 Dec 2002 14:39:51 -0600
From: Kristina Furse <kristina.e.furse_at_vanderbilt.edu>
To: amber list <amber_at_heimdal.compchem.ucsf.edu>
Subject: gB vs. explicit

Hello,

I've been running sander calculations on a large protein (cyclooxygenase dimer
with 2 heme's, 2 arachidonic acids and 8 bog detergents--1118 residues, 18,422
atoms). In the interest of saving compute cycles, I've been using generalized
Born and keeping the 200 crystallographic waters held in place with 1kcal
positional restraints. I recently set up an explicit water simulation as a
control (truncated octahedron, 11A buffer, 6 Na+, SPC/E water...):

  Solute vdw bounding box: 103.139 68.888 84.395
  Total bounding box for atom centers: 130.591 130.591 130.591
  Volume: 1139331.597 A^3 (oct)
  Total mass 646857.976 amu, Density 0.943 g/cc
  Added 28407 residues.

Scary big (29,726 residues, 104,234 atoms)--so I assumed this calculation
would take forever. But I've found that the explicit calculation is running
nearly twice as fast as the generalized Born version! Have you guys really
improved explicit calculations this much??? Could it be a crossover of timing
profiles as the number of atoms gets really large?

Below are input files and the timing section from the output for gB and
explicit calcs. Please let me know if any more information is needed to help
explain this.

Thanks!

Kristina

*NMR restraint refers to a virtual bond between the protein and the heme.

===========================================================
50ps generalized Born on 16 processors SGI Origin
===========================================================
Generalized Born model on Sander 7--equilibration
 &cntrl
   imin=0, nstlim=50000,
   ntx=5, irest=1,
   ntpr=100, ntwx=100, ntwe=100,
   ntf=1, ntc=2, ntb=0,
   tempi = 298.0, temp0 = 298.0,
   ntt=1, tautp=1.0,
   dielc=1.0, cut=12.0, scee=1.2,
   igb=1, saltcon=0.2, gbsa=1,
   ntr = 1, ntrx = 1, nmropt=1,
   nrespa=4
 &end
 &wt type='END' &end
DISANG=Heme_tetherCW.rst
CONSTRAINED RESIDUES
1.0
FIND
O * * *
SEARCH
RES 1119 1319
END
END
------------------------------------------------------------------------------ 

--
   5.  TIMINGS
------------------------------------------------------------------------------
--

|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> 
|                Calc gb radii          26406.29 (23.19% of Gen B)
|                Communicate gb radii    3279.71 ( 2.88% of Gen B)
|                Calc gb diag           38332.51 (33.67% of Gen B)
|                Calc gb off-diag       41634.81 (36.57% of Gen B)
|                Surface area energy     4209.52 ( 3.70% of Gen B)
|             Gen Born time         113862.85 (100.0% of Nonbo)
|          Nonbond force         113862.85 (97.35% of Force)
|          Bond energy               22.54 ( 0.02% of Force)
|          Angle energy              93.08 ( 0.08% of Force)
|          Dihedral energy          523.89 ( 0.45% of Force)
|          FRC Collect time        1502.79 ( 1.28% of Force)
|          Other                    960.63 ( 0.82% of Force)
|       Force time            116966.01 (99.07% of Runmd)
|       Shake time               252.40 ( 0.21% of Runmd)
|       Verlet update time       102.87 ( 0.09% of Runmd)
|       CRD distribute time      523.87 ( 0.44% of Runmd)
|       Other                    215.06 ( 0.18% of Runmd)
|    Runmd Time            118060.20 (100.0% of Total)
| Total time            117777.66 (100.0% of ALL  )

| Highest rstack allocated:     209275
| Highest istack allocated:      76100

|     Setup wallclock           4 seconds
|     Nonsetup wallclock   117775 seconds

===========================================================
50ps truncatedOct on 16 processors SGI Origin
===========================================================
Equilibration of cox dimer, explicit water, 9.0 cut
 &cntrl

  nmropt = 1,
  ntx    = 5,       irest  = 1,       ntrx   = 1,      ntxo   = 1,
  ntpr   = 100,     ntwx   = 100,     ntwv   = 0,      ntwe   = 100,

  ntf    = 2,       ntb    = 2,
  cut    = 9.0,

  ibelly = 0,       ntr    = 0,

  imin   = 0,
  nstlim = 50000,
  nscm   = 0,
  t      = 0.0,     dt     = 0.001,

  temp0  = 298.0,   tempi  = 298.0,
  ig     = 71277,   heat   = 0.0,
  ntt    = 1,
  tautp  = 0.2,
  vlimit = 20.0,

  ntp    = 1,       pres0  = 1.0,     comp   = 44.6,
  taup   = 0.2,

  ntc    = 2,       tol    = 0.00001, watnam = 'SPC ',

 &end
 &ewald

 nbflag  = 1,       skinnb = 2.0,     use_pme = 1,

 &end
 &wt type='END' &end
DISANG=Heme_tetherEXP.rst

------------------------------------------------------------------------------
--
   5.  TIMINGS
------------------------------------------------------------------------------
--

|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> 
|                Ewald setup time           0.24 ( 0.01% of List )
|                Check list validity       73.41 ( 2.22% of List )
|                Map frac coords          106.55 ( 3.22% of List )
|                Grid unit cell            33.30 ( 1.01% of List )
|                Grid image cell           16.39 ( 0.50% of List )
|                Build the list          2985.96 (90.33% of List )
|                Other                     89.79 ( 2.72% of List )
|             List time               3305.74 ( 7.58% of Nonbo)
|                Direct Ewald time      22365.02 (55.52% of Ewald)
|                Adjust Ewald time        297.84 ( 0.74% of Ewald)
|                Finish NB virial        1377.08 ( 3.42% of Ewald)
|                   Fill Bspline coeffs     1471.12 (10.31% of Recip)
|                   Fill charge grid        1949.59 (13.66% of Recip)
|                   Scalar sum              2145.70 (15.03% of Recip)
|                   Grad sum                2664.36 (18.66% of Recip)
|                      FFT communication ti    2690.10 (46.17% of FFT t)
|                      Other                   3136.66 (53.83% of FFT t)
|                   FFT time                5826.76 (40.82% of Recip)
|                   Other                    218.14 ( 1.53% of Recip)
|                Recip Ewald time       14275.68 (35.44% of Ewald)
|                Ewald MPI wait            39.78 ( 0.10% of Ewald)
|                Other                   1925.95 ( 4.78% of Ewald)
|             Ewald time             40282.25 (92.41% of Nonbo)
|          Nonbond force          43588.75 (85.93% of Force)
|          Bond energy               20.79 ( 0.04% of Force)
|          Angle energy              95.94 ( 0.19% of Force)
|          Dihedral energy          413.51 ( 0.82% of Force)
|          FRC Collect time        4650.71 ( 9.17% of Force)
|          Other                   1957.02 ( 3.86% of Force)
|       Force time             50726.97 (78.74% of Runmd)
|       Shake time               629.52 ( 0.98% of Runmd)
|       Verlet update time      1993.48 ( 3.09% of Runmd)
|       Ekcmr time              2910.31 ( 4.52% of Runmd)
|       CRD distribute time     7198.36 (11.17% of Runmd)
|       Other                    962.48 ( 1.49% of Runmd)
|    Runmd Time             64421.12 (100.0% of Total)
|    Other                     13.88 ( 0.02% of Total)
| Total time             64435.09 (100.0% of ALL  )

| Highest rstack allocated:     625408
| Highest istack allocated:    3935320

|     Setup wallclock          14 seconds
|     Nonsetup wallclock    64424 seconds

===========================================================
For comparison, same input file, but LINUX:
50ps truncatedOct on 16 processors LINUX cluster
===========================================================

------------------------------------------------------------------------------
--
   5.  TIMINGS
------------------------------------------------------------------------------
--

|>>>>>>>>PROFILE of Average TIMES>>>>>>>>> 
|                Check list validity     1797.84 (46.11% of List )
|                Map frac coords          201.29 ( 5.16% of List )
|                Grid unit cell            72.72 ( 1.86% of List )
|                Grid image cell           23.69 ( 0.61% of List )
|                Build the list          1736.75 (44.54% of List )
|                Other                     66.86 ( 1.71% of List )
|             List time               3899.40 ( 7.02% of Nonbo)
|                Direct Ewald time      30638.63 (59.31% of Ewald)
|                Adjust Ewald time        248.71 ( 0.48% of Ewald)
|                Finish NB virial        1850.59 ( 3.58% of Ewald)
|                   Fill Bspline coeffs     1580.40 ( 9.68% of Recip)
|                   Fill charge grid        2333.22 (14.30% of Recip)
|                   Scalar sum              1821.88 (11.16% of Recip)
|                   Grad sum                3129.43 (19.17% of Recip)
|                      FFT communication ti    2800.28 (38.89% of FFT t)
|                      Other                   4400.58 (61.11% of FFT t)
|                   FFT time                7200.85 (44.12% of Recip)
|                   Other                    255.29 ( 1.56% of Recip)
|                Recip Ewald time       16321.08 (31.59% of Ewald)
|                Ewald MPI wait            43.95 ( 0.09% of Ewald)
|                Other                   2558.72 ( 4.95% of Ewald)
|             Ewald time             51662.14 (92.98% of Nonbo)
|          Nonbond force          55561.87 (93.49% of Force)
|          Bond energy               13.93 ( 0.02% of Force)
|          Angle energy              83.54 ( 0.14% of Force)
|          Dihedral energy          274.20 ( 0.46% of Force)
|          FRC Collect time        2605.01 ( 4.38% of Force)
|          Other                    891.54 ( 1.50% of Force)
|       Force time             59430.15 (86.25% of Runmd)
|       Shake time               940.36 ( 1.36% of Runmd)
|       Verlet update time      2082.98 ( 3.02% of Runmd)
|       Ekcmr time              1617.09 ( 2.35% of Runmd)
|       CRD distribute time     3733.09 ( 5.42% of Runmd)
|       Other                   1099.76 ( 1.60% of Runmd)
|    Runmd Time             68903.43 (100.0% of Total)
|    Other                     23.63 ( 0.03% of Total)
| Total time             68927.14 (100.0% of ALL  )

| Highest rstack allocated:     599503
| Highest istack allocated:    3935320

|     Setup wallclock          25 seconds
|     Nonsetup wallclock    68905 seconds

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu