AMBER Archive (2008)

Subject: AMBER: MD simulation crashed

From: Aust, Susanne (saust_at_ipb-halle.de)
Date: Wed Sep 17 2008 - 08:10:17 CDT

Hallo Amber user`s,
I tried to run a 10 ns md simulation parallel with my protein in a TIP3P
waterbox. At first I run the minimisation only for the box and the Na ions,
then a minimisation for the whole system (only Zn and the 3 coordinated amino
acids restraint with force of 500). All runs fine. After that I started the
heating MD with weak restraints on the protein ( further high restraints for
Zn and the 3 aa).
Now I will start the production MD. But at first the MD crashed after 836 ps.
Than I minimized the system again and try to start the production MD again,
but now the MD dont`t start.
Here the Parameters for the heating and production MD.
Do you see any failure in my parameters? (under Amber 7 (not parallel) the MD
runs over 1 ns wirh the restraints fine)
I could`nt solve the problem. please help me!
Thank`s a lot!
Susanne

heating MD

protein: 40ps MD with weak restraints on whole protein and strong restraints
on Zn and the coordinated amino acids
 &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 = 2.0,
  nstlim = 40000, dt = 0.001,
  ntpr = 100, ntwx = 100, ntwr = 1000
 /
Hold the protein fixed
10
RES 1 331
END
hold Zn fixed
500.0
RES 332
END
hold coordinated Asp fixed
500
RES 128
END
hold coordinated Glu fixed
500
RES 171
END
hold coordinated His fixed
500
RES 299
END
END

production MD

protein: 10 ns MD with restraints on Zn and Glu, His, Asp
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 2,
taup=2.0, pres0=1.0, ntp=1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 300.0,
  temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 1000000, dt = 0.002,
  ntpr = 2000, ntwx = 2000, ntwr = 20000
 /
hold Zn fixed
500.0
RES 332
END
hold coordinated Asp fixed
500
RES 128
END
hold coordinated Glu fixed
500
RES 171
END
hold coordinated His fixed
500
RES 299
END
END

MD output:

  4. RESULTS
----------------------------------------------------------------------------- 

---

|  # of SOLUTE  degrees of freedom (RNDFP):   56816.
|  # of SOLVENT degrees of freedom (RNDFS):       0.
|  NDFMIN =   56816.     NUM_NOSHAKE =      0     CORRECTED RNDFP =   56816.
|  TOTAL # of degrees of freedom (RNDF) =   56816.
 ---------------------------------------------------
 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 =    2438316
| TOTAL SIZE OF NONBOND LIST =    8642670
vlimit exceeded for step   1897; vmax =    22.2403

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are :    0    2  994 2020 2021

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

 <<md2.out>>
  • application/octet-stream attachment: md2.out
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