Glycam needs different scaling. So, yes, we need pair-specific scaling if ever a carbohydrate (such as, say, ribose) is involved in the model.
:-) Lachele
Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: dcerutti.rci.rutgers.edu [dcerutti.rci.rutgers.edu]
Sent: Wednesday, April 06, 2011 12:58 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] variable 1-4 scaling
If this is a question about being able to tune to factor that scales 1:4
interactions (5/6 for vdW, 1/2 for electrostatics in the AMBER force
fields) then the answer for mdgx is "yes." From the beginning, this factor
has been specifiable by the user. However, if you're referring to some
form of pair-specific scaling that places different factors for different
dihedral interactions, the answer is "no." Wouldn't be too hard to
implement, though, if that is something that people really want to
explore...
Dave
> On Tue, Apr 05, 2011, Jason Swails wrote:
>>
>> Just a quick question -- does NAB have the variable 1-4 scaling added to
>> sander/pmemd?
>
> I'm pretty sure the answer is "no"; same question is now appropriate for
> mdgx
> as well....sigh
>
> ...dac
>
>
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Received on Wed Apr 06 2011 - 10:30:03 PDT
