AMBER Archive (2006)

Subject: AMBER: Gb Na+ ions DNA

From: Conn O'Rourke (
Date: Thu Jul 20 2006 - 10:16:05 CDT

I'm a lowly undergrad who is trying to get to grips with amber and is having
a spot of difficulty.
I have been trying to simulate a DNA chain and Na+ counterions (added using
leap) by way of sander and the
implicit GB approx.
My problem is that on starting md to equilibrate the system the Na+ ions
quickly fly away from the DNA chain.
I have tried a couple of different protocols for equilibriation and
minimisation to no avail.
Is there some obvious reason why this is happening that I am overlooking?
It was suggested to me that it could be something to do with the Na+ GB
Here is the input file for the first stage of equilibriation

  imin = 0, nmropt = 1, ntb = 0,
  igb=1, saltcon=0.0,

  ntx=1, irest=0, ntrx=1, ntxo=1,
  ntpr=100, ntwx=500, ntwv=0, ntwe=0,

  ntc = 2, tol = 0.00001, ntf = 2,

  ntt = 1, temp0 = 300.0, tempi = 100.0,
  tautp = 0.2, vlimit = 25.0, ig = 71277,
  heat = 0.0,

  nstlim = 12500, dt = 0.002,

  cut = 15.0,

  ibelly = 0, ntr = 1,
   type='TEMP0', istep1=0, istep2=1000,
                 value1=10.0, value2=300.0,
   type='TEMP0', istep1=1000, istep2=12500,
                 value1=300.0, value2=300.0,
Hold the DNA - let the ions move
RES 1 24

Any help would be greatly appreciated,
      Conn O'Rourke

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