AMBER Archive (2004)

Subject: AMBER: performance of periodic vs. non-periodic simulation

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Wed May 12 2004 - 14:08:18 CDT

Dear Amber users/developers,

I am have tried to speed up my simulations by switching from a periodic
system with PME to a non-periodic system with a cap of ~300 water
molecules on a ligand binding site. My goal is to calculate relative
ligand binding energies with MM-PBSA and TI.

I first used a non bonded cutoff of 12A for the non-periodic system.
This lead to fluctuations of ~1000 to 2000 kcal/mol of the electrostatic
energy (corresponding to 10% of the total energy) preventing equilibration.
Using a cutoff larger than my system and switching off the update of the
non-bonded pairlist solved this problem - but now the simulations are
significantly slower than for the periodic system (details below).
Is this to be expected?
Do I miss something that could speed up the simulations with the cap
without leading to instability of the electrostatic energy?

Some more details:

I am using sander of AMBER8.

Periodic system:
   size: 50000 atoms, truncated octahedron, cut=8A
   performance: 80ps/day (with dt=0.002)

non-periodic system:
   size: 10000 atoms
   performance: 30ps/day (dt=0.002)

The input for the non-periodic simulation (heating after energy
minimization):

md, warm belly to 300K
  &cntrl
   imin = 0, irest = 0, ntx = 1,
   nstlim = 20000, dt = .002,
   ntpr=100, ntwx=5000,
   ntt = 1, tempi=10.0, temp0 = 300.0, tautp=1.0,
   ntc = 2, ntf = 2,
   cut = 999., nsnb=999999, scee = 1.2,
   ntb = 0,
   ibelly = 1, ntr = 1,
  &end
  &ewald
   eedmeth=4,
  &end
  -- restraint = belly
5.0
  RES a z
END
END
  -- belly
  RES a z
END
END

-----

Best regards,
Oliver 

-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke_at_u.washington.edu
_______________________________________________________________

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