I found this suggested on one of the post about POL3 in amber archive ...
Piotrek
> 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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>>
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Received on Mon Jan 31 2011 - 08:30:06 PST
