[gmx-users] membrane bilayer simulation by OPLS FF

mircial at sjtu.edu.cn mircial at sjtu.edu.cn
Tue Feb 22 06:17:57 CET 2011

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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