Re: [AMBER] distance-dependent dielectric constant minimization

From: Rilei Yu <>
Date: Sun, 6 Dec 2009 15:37:13 +0800 (CST)

Dear Prof. David Case,

Thanks for your remind! I have done many times minimization on a small molecular by changing the constant vlaue:1,2,4,6,8,10. And superpose them with the molecular minimized in explicit water. I found 4 is nearly the best one! What is more I try to change the restraint_wt = 500 to 100.

Thanks for you help again, and I also hope my question and solution can be useful to others!

Best wishes,

Rilei Yu

--- 09年12月6日,周日, case <> 写道:

发件人: case <>
主题: Re: [AMBER] distance-dependent dielectric constant minimization
收件人: "AMBER Mailing List" <>
日期: 2009年12月6日,周日,上午11:03

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.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.


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