you might want to write info to the output more frequently until you solve
the problem, it will show when the energy starts to go up (if it does).
500 is a VERY strong restraint, this might be a problem.
On Wed, Sep 17, 2008 at 9:10 AM, Aust, Susanne <saust.ipb-halle.de> wrote:
> 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>>
>
>
>
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Received on Fri Sep 19 2008 - 03:07:40 PDT
