pressure regulation

From: Andrew Aird <a.aird_at_physik.uni-stuttgart.de>
Date: Wed 24 Jan 2001 19:51:37 +0100

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
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Received on Wed Jan 24 2001 - 10:51:37 PST
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