[gmx-users] about force fields

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Mar 4 18:12:17 CET 2009

Be aware that for n-alkanes longer than ~8 carbons, the standard OPLS  
parameters will fail horribly. You will need to modify dihedrals or  
1-4 interactions as is mentioned in some of the papers below.

William L. Jorgensen, Jeffry D. Madura, Carol J. Swenson, "Optimized  
intermolecular potential functions for liquid hydrocarbons", J. Am.  
Chem. Soc., 1984, 106 (22), pp 6638?6646

George Kaminski and William L. Jorgensen, "Performance of the AMBER94,  
MMFF94, and OPLS-AA Force Fields for Modeling Organic Liquids", J.  
Phys. Chem., 1996, 100 (46), pp 18010?18013

Yooko Tsuchiya, Hiromi Hasegawa and Tetsushirou Iwatsubo, "Prediction  
of the Latent Heat of n-Alkanes Using the Molecular Dynamics Method",  
Jpn. J. Appl. Phys. 42 (2003) pp. 6508-6511

J. R. Elliott Jr.; "Optimized step potential models for n-alkanes and  
benzene", Fluid Phase Equilib. 194-197 161-168 (2002).

--- original message --

Dear All,

I'm planing to do md simulations for n-alkane molecules. I use Gromacs 4.0.4.
I tried to use oplsaa, but I couldn't create .gro and top files.
I created my pdb file using Chem3d. I want to ask if I can use oplsaa for
n-alkanes. And could you suggest me some force fields that can be used for
n-alkanes molecules ?


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