AMBER Archive (2006)

Subject: AMBER: md and implicit solvation

From: Jardas sucuriba (
Date: Tue Oct 24 2006 - 18:57:24 CDT

Hi all

I ran 50 ps of an MD simulation (equilibration phase) using implicit
solvation. However my calculation took 3 days to complete! Is it normal to
take so long? I am really worried because I want to run a production phase
of 1 ns. I wonder if someone could tell me if there is something wrong with
my script or pehaps suggest me modifications to improve it. My system has
around 15000 atoms.

   imin=0, ntx=1,
   dt=0.002, nstlim=25000, igb=5,
   ntpr=100, ntwr=100, ntwx=100, nrespa=2,
   ntb=0, scee=1.2, cut=16.0,
   ibelly=0, ntt=3, gamma_ln=1.0, ntc=2, ntf=2,
   temp0=300.0, tempi=300.0, tol=0.000001,

Thanks a lot

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