AMBER Archive (2004)

Subject: Re: AMBER: MD & running time

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jun 22 2004 - 20:48:03 CDT

> 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. ... it took more than 6 days (>144 hours)
> to finish the run.

> nstlim=500000, dt=0.002, ntx=5, irest=1,

> 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.

With ntx=5 the pressure/density-equilibrated box was restored to
the size of your initial model (7 is the correct value). Thus your
system was subjected to a sudden vacuum, which may explain the
disordering.

A general rule would be, make the first production run short to
validate the mdin file.

Bill
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