AMBER Archive (2009)

Subject: Re: [AMBER] Re: Error on equilibriation of Amber10

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Jun 25 2009 - 07:07:20 CDT

On Thu, Jun 25, 2009, Masakazu SEKIJIMA wrote:
> >
> > After minimization, I tried to equilibrate this system below input file.
> >
> > md1.in (10K, 1fs x 5000steps) : Initial Equilibriation
> >  &cntrl
> >  imin=0, nstlim=10000,
> >  ntf=2, ntb=2, cut=8.0,
> >  ntt=1,
> >  temp0=10.0, tautp=0.2,
> >  ntc=2, tol=0.00002,
> >  ntp=2, taup=0.2,
> >  ntpr=1000, ntwe=1000, ntwx=1000,
> >  /
> >
> > But, I could not execute  equilibriation. Sander of Amber10 only
> > showed below message.
> >
> >          -------------------------------------------------------
> >          Amber 10 SANDER                              2008
> >          -------------------------------------------------------

I am confused: in the files you posted (most of which are irrelevant), you
didn't have the above input file. Instead, you had a "test.csh" script, which
used a "test.in" input that was not the one you list above, and which set
irest=1, which would be wrong for an initial minimization. So, did you
actually use the script above?

The above script might fail because you are trying to do constant pressure
simulation starting from zero K. You need to equilibrate to near room temp.
at constant volume *before* turning on constant pressure.

Also, is there a queuing system involved here? You may be losing error
messages somewhere. Also, when you are seeing problems like this, look
in more detail, by setting ntpr=1 (and nstlim to 10 or so).

...dac

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