On Mon, Sep 14, 2015, Huggins, Esther, C wrote:
> I have a minimization run previous to this, and I set up the ipol to a
> default 1. So how should I equilibrate the system with non polirizable
> potentials? How much is minimized?
>
> The minimization is now resulting in this
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -2.8320E+05 2.3084E+06 3.2614E+07 HW 112
>
> BOND = 0.0043 ANGLE = 0.0113 DIHED = 0.0000
> VDWAALS = 14.4210 EEL = 3141.9935 HBOND = 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000
> EPOLAR = -286353.0043
> Dipole convergence: rms = 0.455E+04 temperature = 0.00
Something is dreadfully wrong here. Your dipole convergence should on the
order of 1.e-5, not 1.e+4. The RMS gradient is enormous...it looks like you
may have hit a "polarization catastrophe." How did you set up your system?
What potentials are you using?
Note that Amber has not been used a lot for simulations with polarizable
potentials, and the potentials using polarizability have not been updated for
a long time. So there may be cases that don't work all that well. If you
really need polarizable potentials, you will need to provide more details
about how you prepared the system.
.....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 14 2015 - 15:00:03 PDT
