On Mon, Sep 14, 2015 at 10:14 AM, Huggins, Esther, C <
esther.huggins273.topper.wku.edu> 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?
When you set the system up with LEaP, do not use a polarizable force field
(e.g., use ff14SB instead of ff02pol... or whatever you used).
In fact, you should *never* set ipol=1 in your input file. This variable
is currently set by tleap inside the prmtop file itself (primarily to stop
users from setting ipol=1 on non-polarizable force fields).
> How much is minimized?
>
Look at the max gradient (GMAX -- 3e7 in your example below). This is way
too large, and will probably cause your system to blow up. Typical values
start out at maybe ~1e2 to 1e3, and should fall to on the order of ~10 or
so before starting simulation. Certainly, your structure is not minimized
well enough.
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
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 51 -2.4814E+07 8.9139E+08 1.2598E+10 HW 112
>
> BOND = 0.0043 ANGLE = 0.0113 DIHED =
> 0.0000
> VDWAALS = 14.4204 EEL = 8934.3235 HBOND =
> 0.0000
> 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> EPOLAR = *************
> Dipole convergence: rms = 0.396E+06 temperature = 0.00
>
This indicates your minimization is failing... perhaps some kind of
polarization catastrophe? What force field are you using?
HTH,
Jason
-
-
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 14 2015 - 09:30:05 PDT
