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.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.email.unc.edu> 写道：
发件人: Robert Duke <rduke.email.unc.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.biomaps.rutgers.edu>
To: "AMBER Mailing List" <amber.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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Dec 05 2009 - 00:30:02 PST
