AMBER Archive (2004)

Subject: AMBER: GBSA frequency update

From: Sergio E. Wong (swon9_at_itsa.ucsf.edu)
Date: Wed Feb 11 2004 - 17:29:10 CST

Hi;

   I'm running a GBSA simulation of a 4000 atom protein (Amber 7 on a
linux platform). The simulation
is taking a bit more than I expected (approximately 8 hours for 13000
steps). I was wondering how frequently are the GB integrals/surface area
calculations performed? I didn't see a way to adjust it in the GBSA
section of the manual. Below is my input to sander. Thanks

-Sergio

Equilibration for implicit solvent
 &cntrl
  imin = 0,
  nmropt = 1,

  ntpr = 1000, ntwx = 1000,
  ntwr = 1000,

  ntf = 2, ntb = 0,
  cut = 12,

  igb =1, gbsa = 1,

  nstlim = 100000,
  t = 0.0, dt = 0.001,

  temp0 = 300.0, tempi = 100.0,
  ntt = 1, dtemp = 0.0,

  ntp = 0,
  taup = 1.0,

  ntc = 2, tol = 0.00001,

 &end

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