AMBER Archive (2008)

Subject: AMBER:

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Fri Jul 04 2008 - 05:34:55 CDT

Hi AMber Users

I am running an first stage md on my system composed of a [protein(part1)
+ (part2) ] solvated and neutralized.

I want part2 to be frozen, so I did using belly. Minimizations went fine.
 When I start the md job:

 &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,
  ibelly=1
 /
Keep protein fixed with weak restraints
10.0
RES 1 796
END
END
Keep part2 fixed with belly
ATOM 1 12180 20821 80124
END
END

The calculation stops with an error :
--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 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 = 0.3338E-14 at 2.509300
| CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1429347
| TOTAL SIZE OF NONBOND LIST = 24009616

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
 0.0
 Etot = -30003.2906 EKtot = 0.0000 EPtot =
-30003.2906
 BOND = 20179.4792 ANGLE = 2640.3486 DIHED =
6628.7767
 1-4 NB = 2527.0010 1-4 EEL = 34717.6394 VDWAALS =
284231.0709
 EELEC = -380927.6064 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.2038E-04
 ------------------------------------------------------------------------------

vlimit exceeded for step 1; vmax = 214.0560

Also in the log file the following message appears
-------------------------------------------
Job started at Fri Jul 4 11:25:26 BST 2008
-------------------------------------------

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 4824 9785 9787

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

--------------------------------------------
Job finished at Fri Jul 4 11:25:46 BST 2008

Any idea if someone has already seen such a pb?
Thanks very much for your help!
Regards
Boutheina

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