[gmx-users] membrane bilayer simulation by OPLS FF

[Dallas Warren]

7 and 8 have nothing to do with OPLS-AA.

As the text tells you, it is the Encad forcefield
(http://www.sklogwiki.org/SklogWiki/index.php/ENCAD_%28force_field%29)

So that then leaves you with the OPLS-AA for you to use :-)

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of mircial at sjtu.edu.cn
> Sent: Tuesday, 22 February 2011 4:18 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] membrane bilayer simulation by OPLS FF
> 
> Dear All:
> 
> I am using OPLS force field (OPLS FF) to do molecular dynamics
> simulations. My system contains DPPC lipid, protein and a small
> molecule. I have the following questions:
> 
> 1, where can I get the topology files for the DPPC lipids?
> 
> 2, How to prepare the topology files for the small molecules? I plan
> to calculate the charges of each atoms by QM method.After I got the
> charges and atom radius, how to prepare the topology files?
> 
> 3, I am using GROMACS 3 and I found there are three all-atom force
> fields there:
> ----------------------------------------------
>   0: GROMOS96 43a1 force field
>   1: GROMOS96 43b1 vacuum force field
>   2: GROMOS96 43a2 force field (improved alkane dihedrals)
>   3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>   4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>   5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>   6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>   7: Encad all-atom force field, using scaled-down vacuum charges
>   8: Encad all-atom force field, using full solvent charges
> -------------------------------------------------
> 
> among them, 6, 7, and 8 are all-atom force fields, right? My question
> is are 7 and 8 also OPLS force fields? If so, which one is
> recommendated to use in lipid-protein complex systems MD simulations?
> What are the differences between 6, 7 and 8.
> 
> Sincerely Yours
> 
> Ruo-Xu Gu
> 
> 
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