AMBER Archive (2006)

Subject: AMBER: some puzzles in equilibration MD

From: Zhihong Yu (
Date: Mon Oct 09 2006 - 08:58:06 CDT

Dear All,

Now I'm running a equilibration MD using PMEMD.MPI (version 9), as usual, I did the equilibration in two step:

inupt file of STEP 1 is as follow:

equilibration md1
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,

  gamma_ln = 5.0, (REMARKS: if I use 1.0 only, the RMS of temperature is 68.96K, AVERAGE is 369.46K, the largest value is 478.01K, so I use 5.0, the result got better, RMS decreased to 26.16K, AVERAGE is 319.46, the largest value is 396.96K. In fact, I think the temperature contorl is not very satisfactory, what should I do? just keep increasing gamma_ln to 10.0 or do something else?)

  nstlim = 20000,

  dt = 0.001, (REMARKS: I used dt = 0.002 at the beginning, but when the MD went to 398 step, error of "vlimit exceeded for step 398; vmax = 128.7932, Coordinate resetting cannot be accomplished, deviation is too large" took place, so I decreased it to dt = 0.001, and restrained the solute only by 2.0 force constant, then the MD could complete. But, when I checked the md out file, I found many many "vlimit exceeded for step" warnings have appeared from beginnig to ending, so I wondered whether this equilibration MD is valid? Can I perform the second NTP equilibration MD based on this MD results? )

  ntpr = 200, ntwx = 200, ntwr = 1000
weakly restain solute in equilibration md1
RES 145 480

    Any advice will be greatly appreciated! Thanks in advance & Best regards!

    yours sincerely, Zhihong Yu

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