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.biomaps.rutgers.edu> 写道：
发件人: case <case.biomaps.rutgers.edu>
主题: Re: [AMBER] distance-dependent dielectric constant minimization
收件人: "AMBER Mailing List" <amber.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.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 Sun Dec 06 2009 - 00:00:02 PST
