AMBER Archive (2009)

Subject: [AMBER] vlimit error after heating restart

From: AL Olson (nmrguy600_at_gmail.com)
Date: Fri Jul 17 2009 - 09:26:05 CDT

Hi, I know this is sort of a used up question in the archive but i cannot
find anyone having the same problem as this.
I minimized my structure holding ligand rigid for many cycles (6000 maxcyc)
and warmed the system (system = protein/ligand/water) to 300K for 20 ps. I
think it went fine, here is the input and last output of that run,

polyA-polyT 10-mer: 20ps MD with res on DNA

 &cntrl

  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 = 1.0,

  nstlim = 10000, dt = 0.002,

  ntpr = 100, ntwx = 100, ntwr = 1000

 /

Keep PMK fixed with weak restraints

20.0

RES 1 189

END

END

 NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 300.34 PRESS =
0.0
 Etot = -58624.3726 EKtot = 15107.1350 EPtot =
 -73731.5075
 BOND = 576.7693 ANGLE = 1326.1141 DIHED =
 1989.0217
 1-4 NB = 666.6005 1-4 EEL = 3493.6884 VDWAALS =
 7716.6018
 EELEC = -90240.1295 EHBOND = 0.0000 RESTRAINT =
739.8263
 EAMBER (non-restraint) = -74471.3338
 Ewald error estimate: 0.4748E-04
 ------------------------------------------------------------------------------

      A V E R A G E S O V E R 10000 S T E P S

 NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 282.99 PRESS =
0.0
 Etot = -60813.2526 EKtot = 14234.8192 EPtot =
 -75048.0719
 BOND = 560.6399 ANGLE = 1275.5163 DIHED =
 1965.1125
 1-4 NB = 668.5587 1-4 EEL = 3503.3026 VDWAALS =
 8281.0984
 EELEC = -92021.3667 EHBOND = 0.0000 RESTRAINT =
719.0665
 EAMBER (non-restraint) = -75767.1384
 Ewald error estimate: 0.6906E-04
 ------------------------------------------------------------------------------

Well from here i naturally tried to restart it with a production time of 100
ps and here is the input and error i get for it,

protein 20ps MD with res lig
 &cntrl

  imin = 0,

  irest = 1,

  ntx = 7,

  ntb = 2,

  pres0 = 1.0,

  ntp = 1,

  taup = 2.0

  cut = 10,

  ntc = 2,

  ntf = 2,

  tempi = 300.0,

  temp0 = 300.0,

  ntt = 3,

  gamma_ln = 1.0,

  nstlim = 50000, dt = 0.002,

  ntpr = 100, ntwx = 100, ntwr = 1000

 /
Keep lig fixed with weak restraints

20.0

RES 189

END

END

 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 7723070
| TOTAL SIZE OF NONBOND LIST = 7723070
vlimit exceeded for step 27; vmax = 24.0912
vlimit exceeded for step 28; vmax = 26.7198
vlimit exceeded for step 44; vmax = 31.3538
vlimit exceeded for step 50; vmax = 28.6795
vlimit exceeded for step 66; vmax = 32.6102
vlimit exceeded for step 70; vmax = 27.8292

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 1 1504 3016 3017

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I understand that something is wrong with my complex but im not sure how to
fix it while keeping my last run good and not re-doing the warming up phase.
  Any thoughts? Thanks

Drew
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