RE: AMBER: Implicit solvent simulation is too slow.

From: Ross Walker <>
Date: Fri, 10 Aug 2007 08:56:32 -0700

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

   28.3 hours / 1ns simulation
   16 Xeon DP 2.8 GHz CPUs
What is the interconnect here? If it is gigabit ethernet then you are
probably running slower than you would on a single node. You should
benchmark here to check. If it is infiniband or myrinet then it is probably
okay you should scale well with GB, especially if you use PMEMD.
   4107 atoms (288 residues protein + 1 ligand)
This is a big system for implicit solvent.
      5 ntpr = 100, ntwx = 100, ntwr = 1000,
Do you really need a restart file every 1000 steps? I would set this closer
to 10,000.
      7 ntb = 0,
      8 taup = 2.0,
taup does nothing when ntb=0.
      9 cut = 10,
Note this is a very small cutoff for an implicit solvent simulation. For
explicit solvent you can go as low as 8 angstroms due to PME but this is not
the case with GB. something like 16 or so would be better here - or
preferably no cut off at all. This will of course make your simulations even
I didn't run explicit solvent simulation yet. (It is waiting its turn in the
But the same simulation done with GROMACS tell me it tooks about 15.4 hour s
for 1ns simulation.
I suspect you are comparing an explicit solvent simulation with an implicit
solvent one which is not a valid comparisson.
All the best
|\oss Walker

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Received on Sun Aug 12 2007 - 06:07:51 PDT
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