Re: [AMBER] distance-dependent dielectric constant minimization

From: case <case.biomaps.rutgers.edu>
Date: Sat, 5 Dec 2009 22:03:47 -0500

On Sat, Dec 05, 2009, Rilei Yu wrote:
>
> My intention is do
> ¬ 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.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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Received on Sat Dec 05 2009 - 19:30:02 PST
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