AMBER Archive (2008)

Subject: Re: AMBER: Heating POL3 Box Troubles

From: Paul Johns (pjohns_at_nd.edu)
Date: Fri Mar 14 2008 - 16:01:22 CDT

> a) does it run if you turn of shake (ntf and ntc)?
It runs a little while longer, but still isn't very successful. The
first 83 steps or so seem OK, then the total energy drops drastically in
the next step. The following step it is listed as **********. Another
thing I noticed was temperature begin to increase rather quickly after
about 78 steps, with as much of a 104 K increase between steps 81 and
82, and ~200 K increase from 82 to 83.

NSTEP = 82 TIME(PS) = 0.016 TEMP(K) = 165.02 PRESS = 0.0
Etot = -46281.1238 EKtot = 3828.8894 EPtot = -50110.0132
BOND = 7792.4103 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 12775.9882
EELEC = -40999.4983 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -29678.9134
Dipole convergence: rms = 0.125E+01 temperature = 82.93
------------------------------------------------------------------------------

NSTEP = 83 TIME(PS) = 0.017 TEMP(K) = 357.00 PRESS = 0.0
Etot = -421854.4605 EKtot = 8283.2468 EPtot = -430137.7073
BOND = 7803.5936 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 12841.3263
EELEC = -41243.6494 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -409538.9777
Dipole convergence: rms = 0.274E+02 temperature = 925.89
------------------------------------------------------------------------------

NSTEP = 84 TIME(PS) = 0.017 TEMP(K) = 35.84 PRESS = 0.0
Etot = -92389131.9871 EKtot = 831.5519 EPtot = -92389963.5390
BOND = 7886.7188 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 12957.0488
EELEC = -39565.5355 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = -92371241.7711
Dipole convergence: rms = 0.542E+03 temperature = ******
------------------------------------------------------------------------------

NSTEP = 85 TIME(PS) = 0.017 TEMP(K) = 87.61 PRESS = 0.0
Etot = ************** EKtot = 2032.7980 EPtot = **************
BOND = 7614.8972 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 12901.8483
EELEC = 587542.2211 EHBOND = 0.0000 RESTRAINT = 0.0000
EPOLZ = **************
Dipole convergence: rms = 0.479E+04 temperature = ******
------------------------------------------------------------------------------

vlimit exceeded for step 85; vmax = 349.2428

> b) look at the trajectory for the first few steps, which parts move fast?
Without shake, there are only very small movements, as expected. With
shake, it looks like throughout the box everything moves with the same
speed. Rotations seem a bit faster than translations. After only about
30 steps or so, it seems as if the rotations mostly stop, and the whole
box begins to translate more or less as a single unit, with the
exception of a few spots, where it seems like I have mini-blackholes.
The nearby waters basically get sucked into a single point
> c) start at tempi=10, maybe something goes wrong when your system has
> zero
> kinetic energy and is also perfectly minimized
This makes no difference. Same errors.
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