AMBER Archive (2003)

Subject: AMBER: Ewald problem

From: Shuang Ding (sd517_at_nyu.edu)
Date: Wed Jul 30 2003 - 11:08:55 CDT

Dear Amber User,

I'm running a MD simulation of damaged DNA with base adduct. The system got blow up at about 600ps with error message "SHAKE cannot be accomplished". Then I try to restart the MD before the blowup and reassign velocities, the production stopped at around 100ps with error "EWALD BOMB in subroutine ewald_list, volume of ucell too big, too many subcells, list grid memory needs to be reallocated, restart sander".
What dose the error message mean? Can I use longer cutoff(like cut=16) without PME in the MD simulation to solve this problem?

Here is my imput file for production:
&cntrl
  ntx = 7, irest = 1,
  ntpr = 200, ntwx = 1000, ntwv = 0, ntwe = 0,

  ntf = 2, ntb = 2, dielc = 1.0,
  cut = 9.0,

  ibelly = 0, ntr = 0,

  imin = 0,
  nstlim = 200000,
  t = 0.0, dt = 0.001,

  temp0 = 300.0, tempi = 300.0,
  ig = 71277, heat = 0.0,
  ntt = 1, dtemp = 0.0,
  tautp = 1.0,

  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 1.0, npscal = 1,

  ntc = 2,
 &end

Thanks a lot for your help.
shuang

 
 

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