dear andrew
To echo what Jim said, such fluctuations may seem alarmingly large, but
what I've found is that over a long time the average pressure will
converge (slowly) to what you set it too. Also, the size of pressure
fluctuations should scale as the inverse square root of the number of
molecules. I have checked this out a bit and it seems to hold true. That
is, bigger water boxes have smaller pressure fluctuations and if you try
a number of system sizes and plot things it looks about right.
hope this helps
Tom D
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
> Universität Stuttgart
> Pfaffenwaldring 57
> D 70569 Stuttgart
> e-mail: a.aird_at_physik.uni-stuttgart.de
> ---------------------------------------------------
>
Received on Thu Jan 25 2001 - 08:50:13 PST
