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_.kaist.ac.kr
sp1020.gmail.com
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Received on Sun Aug 12 2007 - 06:07:50 PDT
