[gmx-users] Re: about ffgmxnb.itp and lipid.itp (nanyu101)

[Wei Fu]

Hi, Wu,

   We have disscussed this problem. see bellow:

Fuwei

******************************************

      Ms. Wei Fu, Ph.D.
      State Key Laboratory of Drug Research     
      Shanghai Institute of Materia Medica
      Chinese Academy of Sciences         
      294 Taiyuan Road
      Shanghai, 200031        
      P.R. China
      wfu at mail.shcnc.ac.cn 
      wfu at iris3.simm.ac.cn 


Hi all,

Marc Baaden's warning about the somewhat unexpected behavior of grompp 
when
having multiple atomtypes and non-bonded entries applies to using 
lipid.itp
too. In the way I set it up, the LJ interaction matrix in the GROMOS 
based
force fields (ffgmx in this case) is overwritten with standard 
combination
rules. I don't yet know what the effect is of this. It means the force 
field
isn't used the way it was designed. On the other hand, nearly all 
published
simulations on membrane proteins with gromacs will have used the 
combination
rules for the protein part instead of the GROMOS values, often without
disastrous consequences.

To use the protein-protein GROMOS LJ parameters, the contents of 
lipid.itp
should be copied into the ffgmx* files as Marc described. It should be
possible to test the differences on simulations of high-resolution 
membrane
protein structures.

Peter