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 Fri Jan 28 2011 - 11:30:04 PST
