AMBER Archive (2003)

Subject: MD problem

From: Shuang Ding (sd517_at_nyu.edu)
Date: Thu May 29 2003 - 15:47:20 CDT

Hi,

I'm running an MD simulation of a DNA 11-mer damaged covalently with a bulky adduct attached to one base. However the simulation was stopped after 50ps of production in AMBER 7 with error message:
" vlimit exceeded for step 50582; vmax = 26.05232686120750
  vlimit exceeded for step 50583; vmax = 24.16632764793692
 EWALD BOMB in subroutine ewald_list
 volume of ucell too big, too many subcells
 list grid memory needs to be reallocated, restart sander"

Equilibration was performed normally as in the DNA tutorial (minimized for 1000 steps of steepest descent, followed by 50ps dynamics with DNA fixed to relax the water, then minimized for 1000 additional steps of steepest descent, follow by 3ps dynamic with 25kcal/mol restraints on the DNA, five rounds minimization of 600 steps with restraint reduced by 5kal/mol each round, from 20 to 0kal/mol. Finally heated up from 10k to 300k over 40ps, and additional 20ps unrestrained dynamics for equilibration.)

This happens after 58ps of production in AMBER6 too, with error message:
“ vlimit exceeded for step 58303; vmax = 187.5334023293732
 COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
  DEVIATION IS TOO LARGE
  NITER, NIT, LL, I AND J ARE : 0 4 63 172 173”

This is my input file for both AMBER 6 and 7:
&cntrl
  ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
  ntwprt = 0, ntwr = 500,

  ntf = 2, ntb = 2, dielc = 1.0,
  cut = 12.0, nsnb = 10,
  scnb = 2.0, scee = 1.2,

  ipol = 0,
  ibelly = 0, ntr = 0,

  imin = 0,
  nstlim = 200000,
  nscm = 1000,
  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,
  vlimit = 20.0,

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

  ntc = 2, tol = 0.000001,
  &end

Could anyone give some suggestion to solve this problem? Thanks a lot.