AMBER Archive (2004)

Subject: AMBER: MD & running time

From: bybaker_at_itsa.ucsf.edu
Date: Tue Jun 22 2004 - 13:11:58 CDT

Hello, Amber:

I try to run a molecular dynamics on my wide type protein. Referring to
the tutorial, I have the system equilibrated through two stages, first
only allow the temperature to increase from 0K to 300K, while the
pressure to be kept constant. Then the system was equilibrated using
pressure and temperature control to adjust the density of water to
experimental values. After the two steps of equilibration, the system was
subjected to a production run. As nanoseconds length simulations are
typically required for publication level work, I set the number of time
steps to 500,000 steps. This time, it took more than 6 days (>144 hours)
to finish the run. Is this usual for molecular dynamic? Are there anyways
to speed up the process? Or I should reduce the size of water box that
is used to solvate the protein?

The protein contains 220 amino acids (3376 atoms in total). It was
solvated with ‘WATBOX216’ and buffering distance is ‘10’, which added
9631 residues to the system. The system was neutralized by adding two
‘Na+’ in tleap. I am using Amber7.

Here is the input file:
 
Initial molecular dynamic production run 1: constant pressure constant temp
 &cntrl
  nstlim=500000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000,
  ntwx=5000,
  temp0=300.0, ntt=1, tautp=2.0,
  ntb=2, ntp=1,
  ntc=2, ntf=2,
  nrespa=1,
 &end

After the run, I notice that there are significant changes on the protein
structure, especially at the helix regions. Most helixes are disordered
and turn into loops.

Thanks for any advice and suggestions.

Regards

Bo Yang

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