AMBER Archive (2009)

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

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sun Dec 06 2009 - 01:37:13 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 <case_at_biomaps.rutgers.edu> 写道：

发件人: case <case_at_biomaps.rutgers.edu>
主题: Re: [AMBER] distance-dependent dielectric constant minimization
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
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_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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