AMBER Archive (2004)

Subject: Re: AMBER: MD & running time

From: Linda Prengaman (
Date: Tue Jun 22 2004 - 14:12:00 CDT

I'm not sure what your computational system for running MD is like, but in
general I would say yes, so long a running time is to be expected.
Reducing the size of the periodic box may help, as well as reducing the
cutoff. However, reducing these may affect the accuracy of your
simulation. You could cut down the number of steps you are running the
system for, depending on how long it takes your system to stablize itself
(Etot should hover around the same value). I'm not sure I can offer any
advice about the confirmational changes your system is going through, but
you might want to double check everything. Good luck.
Linda Prengaman

> 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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