Re: [AMBER] distance-dependent dielectric constant minimization

From: Rilei Yu <>
Date: Sat, 5 Dec 2009 16:21:58 +0800 (CST)

Dear amber users,

Based on Prof. David' suggestion, I did some revision in the 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.

  imin   = 1,
  maxcyc = 1000,
  ncyc   = 500,
  ntb    = 0,
  igb    = 0,
  ntr=1, restraint_wt=500.0, restraintmask=':1-432.CA',
  cut    = 12,

I am really appreciated for your time!
Rilei Yu

--- 09年12月1日,周二, Robert Duke <> 写道:

发件人: Robert Duke <>
主题: Re: [AMBER] distance-dependent dielectric constant minimization
收件人: "AMBER Mailing List" <>
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" <>
To: "AMBER Mailing List" <>
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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Received on Sat Dec 05 2009 - 00:30:02 PST
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