Subject: solvation model for simulation of macromolecule

From: water Miller <[email-masked]>
Date: Sat, 24 Feb 2001 13:51:02 -0800 (PST)

Hello everyone,

I am very new to the field, hope someone could provide

help, suggestion or comments. thanks a lot!

In reference, there are about 3 kinds of models:

(1)Discrete model: 
   Most or all solvent molecules explicitly interact  
 with solute in MM force field, but too expensive for 
  computation.
   My question: as the development of computation   
hardware and software9algorithum), it this still a   
problem?  At least, I have seen a lot of papers   
using this approach, eg. QM/MM.

(2)Continum model:
   the solvent is treated as a dielectric continuum,  
 providing a "reaction field". The solute and solvent 
  polarizes each other. the most advantageof this   
model is cheap for computing, but it neglects the 
   specific interactions between solvent and solute.

    My question: is this a serious problem? will the  
    dynamics by this approach be very different from  
    discrete model?   

(3)hybrid models:

   two-layer: discrete/QM for a few (1st shell)
solvent
            + continuum/MM       

   three-layer: discrete/QM for 1st shell solvent
              + 2nd layer solvent(explicit)/MM
              + continnum/MM
   
   My question: is this easy to implement for a   
dynamics simulation, MC or MD?

My personal impression from some papers: the discrete
model is more popular, and easy to implement, also
usually gives good results(compared with experiments).
is there any comment? 

Thanks a lot in advance!

Water

__________________________________________________
Do You Yahoo!?
Get email at your own domain with Yahoo! Mail. 
http://personal.mail.yahoo.com/