Which structure you used for your reference? I normally use structure from
previous equilibration step as reference instead of starting structure.
Hai Nguyen
On Wed, May 16, 2012 at 6:26 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
> Dear Amber users,
>
> During my MD run I got such as error about shake, please see below
>
>
> ---------------------------------------------------
> 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 = 1468479
> | TOTAL SIZE OF NONBOND LIST = 21413472
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -351381.5964 EKtot = 0.0000 EPtot = -
> 351381.5964
> BOND = 251.5921 ANGLE = 1235.1768 DIHED =
> 1604.5703
> 1-4 NB = 1314.9823 1-4 EEL = 13887.0078 VDWAALS =
> 56065.2558
> EELEC = -425740.1815 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.6214E-04
>
> ------------------------------------------------------------------------------
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 8 14 192 190
>
>
> my input file was:
>
>
> equilibration
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 9,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 10.0, vlimit=5,
> nstlim = 10000, dt = 0.002,
> ntpr = 50, ntwx = 50, ntwr = 50
> /
> Keep protein with the weak restraints
> 10.0
> RES 1-380
> END
> END
>
> minimization steps worked without any problems, should I change something
> in this input file?
>
> /Urszula
>
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Received on Wed May 16 2012 - 16:30:03 PDT
