box size & 1st equilibrium

From: yuann <>
Date: Fri 28 Jun 2002 14:16:51 +0800 (CST)

Dear AMBER users:
  I've encountered blow up problem when I do a dynamics run
(1st equilibrium) with constant pressure PBC's. (I'd like to
equilibrate the density of mysystem: (DNA+WAT+Na+) generated by Leap).
  The error message is:

  Weirdly, it just appears when I turn on NTR with force restrain(500),
  and the dynamics job works smoothly with turning on ibelly.
  However, I'm warned in mdout when using ibelly, and ibelly doesn't seem
  to be suitable for DNA...?

  I also checked the vdw bounding box of solute & whole box as follows,

> solvatebox dna WATBOX216 {3.7, 3.5, 3.8} 1.0
  Solute vdw bounding box: 27.702 33.472 44.833
  Total bounding box for atom centers: 35.102 40.472 52.433
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 37.968 43.772 55.471 angstroms.
  Volume: 92188.719 A^3
  Total mass 39673.368 amu, Density 0.715 g/cc
  Added 1792 residues.

  The cut off distance is 9A. I took notice of the same problem in
  this Mail Reflector Archive, so I also edited the vdw in the bottom of
  inpcrd file by increasing 3A to each axis. The error message above was
  still appeared at around 13ps(the density is still < 1).

  Thanks for your help!

  Best Regards,

(here is the mdin of this dynamics job)
   imin=0, dt=0.002, ntr=1, ntb=2, nstlim=10000,
   irest=0, ntx=1, t=0.000,
   ntc=2, tol=0.0005, ntf=2,
   ntt=1, temp0=100.0, tempi=0.0, tautp=1.0,
   ntp=1, taup=0.2,
   ntpr=50, ntwr=50, ntwx=50,
Group input for restrained DNA
RES 1 24
Received on Thu Jun 27 2002 - 23:16:51 PDT
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