AMBER Archive (2008)

Subject: Re: AMBER: Heating POL3 Box Troubles

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 18 2008 - 00:30:48 CDT

On Mon, Mar 17, 2008, Paul Johns wrote:

> 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

Just to be sure: does your system pass the polarizable_water test? You
might look at the example in that test, and see if you see something different
from what you have in your files.

Also, what does a 5 step (say) minimization look like (set ntpr=1)?

You also might run the md simulation for 25 steps or so. Does it ever
straighten itself out? (It looks like vmax is doing its job). Can you check
the masses in the prmtop file?

Just guessing in the dark here. You might (re-)post the exact commands you
used to create the initial prmtop and coordinate files.

...dac

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