[AMBER] constant volume

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Wed, 11 Aug 2010 10:06:26 +0200

Hi,

I am equilibrating my system raising the temperature from 0 to 300K - I want
to start by also equilibrating the pressure doing my simulation in NVT
enzemble so I set my variables using constraits on my protein backbone (10
kcal/mol)

 ntx = 1,
  ntb = 1,
  cut = 12.0,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 10000, dt = 0.001

when I look at my results in VMD the only thing that has really changed is
the box which is no longer square but a strange form. Furthermore if I plot
volume and pressure from the output file the volume is increasing and the
pressure is at 0 - do I need to specify some other parameters for the NVT? I
have also looked at the starting position from the prmtop and rst file and
they look fine. The gradient from the minimization was 10¯2. I use the rst
file from the minimization as -ref for the constraints but that should not
give any problems I would pressume.
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Received on Wed Aug 11 2010 - 01:30:04 PDT
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