AMBER Archive (2009)

Subject: Re: [AMBER] distance-dependent dielectric constant minimization

From: case (case_at_biomaps.rutgers.edu)
Date: Sat Dec 05 2009 - 21:03:47 CST

On Sat, Dec 05, 2009, Rilei Yu wrote:
>
> My intention is do
> Â distance-dependent dielectric constant minimization.
> (distance-dependent dielectric constant =4r). Can anyone check my
> file? I have run it successfully, but I still I did what I really want
> to do.
>
>
>  &cntrl
>   imin   = 1,
>   maxcyc = 1000,
>   ncyc   = 500,
>   ntb    = 0,
>   igb    = 0,
>   ntr=1, restraint_wt=500.0, restraintmask=':1-432_at_CA',
>   cut    = 12,
>   dielc=4,
>   &end
>  &ewald
>     eedmeth=5,
>  &end  

This looks OK to me; I continue to think that your restraint_wt is much too
large. You can check some things: compare the electrostatic energies as a
function of dielc (they should just scale). If you want to be sure you
have a distant-dependent dielectric, run a very small molecule that you
can do "by hand" to compare.

...dac

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