AMBER Archive (2003)

Subject: RMSD fluctuation too much

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Thu May 08 2003 - 10:02:43 CDT

Hi, AMBER fans:
  I tried to run 1 nm MD on a protein-ligand complex in vacco. After
465ps, the job stopped without any error message in the output file. I
restarted the job as a continuous MD run (ntx=5,irest=1), 100ps later
the job stopped again. I don't know what cause the job to stop. I used
carnal to check the RMSD and found something abnormal. At the end of
first MD run, RMSD is fluctuated around 3 A. After restarting MD, at the
beginning of the second MD run, RMSD goes down to 1.5 A. The RMSD should
fluctuated aroung 3 A in the second run if my system is stable because
the coordinates and velocity were read from the restart file from the
previous run. Could anybody give me some hints to solve the problem.
 Thank you in advance, Youyi.
 This is the input file:

 &cntrl
  nmropt = 0,
  ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
  ntpr = 1000, ntwx = 1000, ntwv = 0, ntwe = 0,

  ntf = 1, ntb = 0,
  cut = 13.0, nsnb = 10, dielc=4.0

  ibelly = 0, ntr = 0,

  imin = 0,
  nstlim = 535000,
  nscm = 500,
  dt = 0.001,

  temp0 = 300.0, tempi = 300.0,
  heat = 0.0,
  ntt = 1,
  tautp = 2.0,
  vlimit = 20.0,

  ntc = 1, tol = 0.00001,
 &end

 &ewald
   eedmeth=5,
 &end