AMBER Archive (2009)

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

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sat Dec 05 2009 - 02:21:58 CST

Dear amber users,

Based on Prof. David' suggestion, I did some revision in the min.in file. 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_at_CA',
  cut    = 12,
  dielc=4,
  &end                                                                         
 &ewald                                                                       
    eedmeth=5,                                                                
 &end  

I am really appreciated for your time!
Regards,
Rilei Yu

--- 09年12月1日，周二, Robert Duke <rduke_at_email.unc.edu> 写道：

发件人: Robert Duke <rduke_at_email.unc.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1日,周二,下午9:06

Also please note that this option is not supported by pmemd.
Regards - Bob Duke
----- Original Message -----
From: "case" <case_at_biomaps.rutgers.edu>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Tuesday, December 01, 2009 7:48 AM
Subject: Re: [AMBER] distance-dependent dielectric constant minimization

> On Tue, Dec 01, 2009, Rilei Yu wrote:
>>
>> Thanks for your remind, I went back and read the manual again it
>> just gives me a very brief introduce as" Dielectric multiplicative
>> constant for the electrostatic interactions. Default is 1.0. Please
>> note this is NOT related to dielectric constants for generalized
>> Born simulations.". After read, I still do not know how to run the
>> distance-dependent dielectric constant minimization. I ever read similar
>> paper people did such minimization for some special purpose. But they
>> never said how they did it.
>
> Sorry, I haven't used a distance-dependent dielectric in many years.  Look
> at the eedmeth variable, (and be sure that this is what you really want to
> do--it is no longer in common use.)
>
> ...dac
>
>
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