Re: pressure regulation

From: jim caldwell <caldwell_at_heimdal.compchem.ucsf.edu>
Date: Wed 24 Jan 2001 11:47:48 -0800 (PST)

Actually those kind of fluctuations aren't surprising
especially is the system isn't very well equilibrated
yet. Run a couple of hundred picoseconds of MD first
to equilibrate your system. Also the average pressure
and the RMS deviation are much better indicators that
the absolute instantaneous value.

jim

On Wed, 24 Jan 2001, Andrew Aird wrote:

> Hello Amber users
>
> I'm trying to do a simulation using sander (Amber6):
>
> - periodic boudary conditions (constant pressure)
> - my water box consists of 347 water molecules (I'm simulationg only one ion!!)
> - 300K
> - the pressure should be kept at 1 bar (default)
> - box size 25*25*25 Angstroms
>
> The pressure in the md.out file fluctuates between -300 bar and +400 bar.So I
> guess there must be something wrong with my setup. Here's my md.in file. I've
> looked at it several times, but I can't find anything that would explain the
> fluctuations...
> I hope it's nothing too obvious!!!
>
>
> MD with solvent, 5 Angstrom cutoff, temperature ramp
> &cntrl
> igb = 0, ntb = 2, ntpr = 100, ntwx = 100, nmropt = 1,
>
> cut = 5.0, ntc = 2, ntp = 1,
>
> tempi = 0.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
>
> imin = 0,
> nstlim = 50000, dt = 0.002,
> &wt
> type = TEMP0, istep1 = 0, istep2 = 1000,
> value1 = 0.0, value2 = 20.0,
> &end
> &wt
> type = TEMP0, istep1 = 1001, istep2 = 2000,
> value1 = 20.0, value2 = 50.0,
> &end
> &wt
> type = TEMP0, istep1 = 2001, istep2 = 7000,
> value1 = 50.0, value2 = 250.0,
> &end
> &wt
> type = TEMP0, istep1 = 7001, istep2 = 9000,
> value1 = 250.0, value2 = 280.0,
> &end
> &wt
> type = TEMP0, istep1 = 9001, istep2 = 10000,
> value1 = 280.0, value2 = 300.0,
> &end
> &wt
> type = END
> &end
> &rst
> iat = 0,
> &end
> END
>
> Thanks a lot in advance...
>
> Andrew
>
>
> ---------------------------------------------------
> Andrew Aird
> 3.Physikalisches Institut
> Universitšt Stuttgart
> Pfaffenwaldring 57
> D 70569 Stuttgart
> e-mail: a.aird_at_physik.uni-stuttgart.de
> ---------------------------------------------------
>


----------------------------------------------------------------------------
James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-502-1411
Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
513 Parnassus Avenue (video) farbauti.compchem.ucsf.edu
University of California (netmeeting)
San Francisco, CA 94143-0446
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Received on Wed Jan 24 2001 - 11:47:48 PST
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