AMBER Archive (2008)

Subject: Re: AMBER: Heating POL3 Box Troubles

From: Paul Johns (pjohns_at_nd.edu)
Date: Mon Mar 17 2008 - 15:07:02 CDT

David A. Case wrote:
> I think you have to set indmeth=1 (not the default of 3) until you have an
> equilibrated sample. If you look at the dipole temperatures you get, you
> will probably see crazy behavior there. In spite of what Thomas suggested,
> don't turn off SHAKE.
So I set indmeth = 1, and I still don't get good results. Even the first
step results in ********* being listed as the temperature, as well as
extremely high energies. Are there other Polarizable potentials
variables that I would need to change to get this working?

NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -43108.5619 EKtot = 0.0000 EPtot = -43108.5619
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 13200.1569
EELEC = -40986.0304 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -15322.6885
Dipole convergence: rms = 0.456E-04 iters = 8.00
------------------------------------------------------------------------------

NSTEP = 1 TIME(PS) = 0.000 TEMP(K) =********* PRESS = 0.0
Etot = 166361094.1462 EKtot = 166404202.7081 EPtot = -43108.5619
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 13200.1569
EELEC = -40986.0277 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -15322.6912
Dipole convergence: rms = 0.456E-04 iters = 8.00
------------------------------------------------------------------------------

vlimit exceeded for step 1; vmax = 190.3043

NSTEP = 2 TIME(PS) = 0.000 TEMP(K) =********* PRESS = 0.0
Etot = 151283636.1397 EKtot = 151223744.5244 EPtot = 59891.6153
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 156148.8784
EELEC = -66237.3762 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -30019.8869
Dipole convergence: rms = 0.947E-04 iters = 20.00
------------------------------------------------------------------------------

vlimit exceeded for step 2; vmax = 25.7249

NSTEP = 3 TIME(PS) = 0.001 TEMP(K) =334402.27 PRESS = 0.0
Etot = 5203620.5424 EKtot = 5172302.4338 EPtot = 31318.1085
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 124291.7005
EELEC = -65716.0400 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -27257.5520
Dipole convergence: rms = 0.833E-04 iters = 17.00
------------------------------------------------------------------------------

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