On Mon, 2014-11-10 at 21:25 +0800, ZHAO Ruisheng wrote:
> My heating process proceeds only one ster before stoping, and no
> warning message appeard in the output file. This is the lase few lines
> of the output file,
> | # of SOLUTE degrees of freedom (RNDFP): 74358.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 74358. NUM_NOSHAKE = 0 CORRECTED RNDFP = 74358.
> | TOTAL # of degrees of freedom (RNDF) = 74358.
> ---------------------------------------------------
> 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 = 1631015
> | TOTAL SIZE OF NONBOND LIST = 11550524
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = -156610.0437 EKtot = 0.0000 EPtot = -156610.0437
> BOND = 171.1398 ANGLE = 584.1696 DIHED = 3001.2537
> 1-4 NB = 1024.2270 1-4 EEL = 8815.2086 VDWAALS = 29486.5644
> EELEC = -199692.6067 EHBOND = 0.0000 RESTRAINT = 0.0000
> Ewald error estimate: 0.1163E-03
> ------------------------------------------------------------------------------
> This is input file
> HRP-H2O2 heat
> &cntrl
> imin=0, irest=0, ntx=1, ntb=1,
> cut=10.0, ntr=1, ntc=2, ntf=2,
> tempi=0.0, temp0=300.0, ntt=3,
> ig=-1, gamma_ln=2.0, nstlim=20000,
> dt=0.002, ntpr=100, ntwx=100, ntwr=1000
> /
> Keep Protein fixed
> 10.0
> RES 1 309
> END
> END
> In addition, my system had been minimized (three minimization), and I
> have check the structure of the system with "check" commond of
> cpptraj , and no two atoms sit too closely. Anyone can give me some
> useful suggestions to solve this problem?
What program are you using? What version of Amber is it from? How many
updates have been applied to that version?
The last bit of advice is to look at the standard error stream (it is
usually printed to the screen, but in some cases it may be redirected to
another file) -- the error may be printed there instead (there are a
small number of errors for which this is true).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 10 2014 - 06:00:03 PST
