AMBER Archive (2007)

Subject: AMBER: Implicit solvent simulation is too slow.

From: SeungPyo Hong (sp1020_at_gmail.com)
Date: Fri Aug 10 2007 - 07:42:11 CDT

Dear amber users,
Go to the point, I found my Implicit solvent calculation is too slow.
Could anybody tell me whether my simulation is problematic or Amber itself
is slower than I had expected?

It tooks about 28.3 hours for 1ns simulation under following condition:

   28.3 hours / 1ns simulation
   16 Xeon DP 2.8 GHz CPUs
   4107 atoms (288 residues protein + 1 ligand)
   implicit solvent simulation

The run option of the MD is this:
      1 Equilibration Molecular Dynamics: name (Implicit Solvent Model)
      2 &cntrl
      3 nstlim = 50000, dt = 0.002,
      4 tempi = 300.0, temp0 = 300.0,
      5 ntpr = 100, ntwx = 100, ntwr = 1000,
      6 imin = 0, irest = 1, ntx = 7,
      7 ntb = 0,
      8 taup = 2.0,
      9 cut = 10,
     10 ntr = 0,
     11 ntc = 2, ntf = 2,
     12 igb = 1,
     13 ntt = 3, gamma_ln = 1.0
     14 /

I didn't run explicit solvent simulation yet. (It is waiting its turn in the
queue...)
But the same simulation done with GROMACS tell me it tooks about 15.4 hour s
for 1ns simulation. 

-- 
--------------------------------------------------
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many object.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
sphong__at_kaist.ac.kr
sp1020_at_gmail.com

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