I am curious to know why you have applied SHAKE during minimization (i.e. *
ntc=2,*).
Hirdesh
On Sat, Jan 29, 2011 at 12:31 AM, <piotrek.vega.umcs.lublin.pl> wrote:
> Dear Amber Users,
>
> I have some problems with minimizing system with POL3 water model.
> I tried to find all previous posts about POL3, however none of the tricks
> helped me,... so I would greatly appreciate your help:
>
> 1) the amber passed the polarizable_water model test
> ( in tests/polarizable_water)
>
> 2) the pure bulk POL3 water model crashes with NaN energies
>
> input created as follows:
> loadoff solvents.lib
> loadamberparams frcmod.pol3
> WAT = PL3
> xx = copy PL3
> solvateBox xx POL3BOX 10
> saveAmberParmPol xx test.top test.inp
>
> minimization-input:
> &cntrl
> imin=1,
> maxcyc=1000,
> ncyc=500,
> ntb=1,
> cut=10,
> ntpr=100,
> ntc=2,
> ipol=1,
> /
> (I turned shake on as suggested in some posts, but it did not help)
> output (job crashed with Segmentation fault)
> NSTEP ENERGY RMS GMAX NAME
> NUMBER
> 1 NaN NaN 0.0000E+00 O 1
>
> BOND = 136072.7823 ANGLE = 0.0000 DIHED =
> 0.0000
> VDWAALS = NaN EEL = NaN HBOND =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> EPOLAR = NaN
> Dipole convergence: rms = NaN temperature = 0.00
>
>
> 3) energy in protein with POL3 oscillate between negative and positive
> 10^60 or something like that:
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 200 4.5623E+80 6.1029E+83 1.5765E+86 HVC2 408
>
> BOND = 565.7465 ANGLE = 5864.3112 DIHED =
> 6390.4178
> VDWAALS = 560064.1469 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = ************* 1-4 EEL = -752151.1078 RESTRAINT =
> 0.0000
> EPOLAR = *************
> Dipole convergence: rms = 0.150E+46 temperature = 0.00
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 300 -1.2711E+80 9.5867E+82 2.9551E+85 HVC2 408
>
> BOND = 565.7471 ANGLE = 5864.3112 DIHED =
> 6390.4178
> VDWAALS = 560064.1414 EEL = ************* HBOND =
> 0.0000
> 1-4 VDW = ************* 1-4 EEL = -396325.9653 RESTRAINT =
> 0.0000
> EPOLAR = *************
> Dipole convergence: rms = 0.454E+45 temperature = 0.00
>
>
>
> Thanks,
> Piotr
>
>
>
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Received on Sat Jan 29 2011 - 01:00:03 PST
