it might be because you are heating from 0K to 300K very quickly.
you might try slower heating, or assign tempi of at least 200K, maybe
even 300K (it depends on your system and how careful you need to
be with equilibration, but it's something to at least try in order to identify
the problem).
the initial bond and vdw energies are really high - are you sure the
minimization went as well as you think? is the initial energy here the same
as the final energy from minimization? the vdw seems too high, even with
explicit water (which usually has large vdw but even larger negative
electrostatic)
carlos
On Fri, Jul 4, 2008 at 6:34 AM, Boutheina Kerkeni <b.kerkeni.ucl.ac.uk> wrote:
> 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
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jul 06 2008 - 06:07:44 PDT
