[gmx-users] Questions on combination of Berger's united-atom force field for lipid and OPLS_AA force field for protein

[mircial at sjtu.edu.cn]

Dear All:

I am using GROMACS package to simulate membrane proteins. I plan to  
use Berger's united atom force field (Berger's UA FF) for lipids and  
OPLS_AA force field (OPLS_AA FF) for proteins.

I have read the guide post kindly by Prof. Dr. Chris Neale in previous  
mailing lists very carefully. According to his guide, the following  
steps are needed:

1). Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after  
changing c6/c12
to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected by
pope.itp
   - sigma   = (c12/c6)^1/6
   - epsilon = c6/(4*sigma^6)

2). Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after  
changing c6/c12
to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all  
reference
to OW to opls_116 (opls spc water oxygen) and simply removed any with  
reference
to HW as it will be zero regardless.

3). Added [dihedraltypes] from lipid.itp to ffoplsaabon.itp.
   - Prior to running ensure that the non-RB dihedral does not exist for these
groups.

4). make a topology file like this:

My questions are as follows:

1, Berger's United atom force field scale LJ1-4 interaction by 0.125  
and scale Coulombic1-4 interaction by 1.0. OPLS_AA FF scale both of  
them by 0.5, right? From the above changes, I find that the changes of  
the sigma or epsilon (or c6 and c12) is only associate with the LJ1-4  
interaction. So, how the Coulombic1-4 interaction is scaled properly?  
Do I need additional changes?

2, the non-bond interactions between the atoms from the lipid and the  
atoms from the protein are need to be calculated, right?  My question  
is how these interactions are calculated? Does the changes in the  
[atomtypes]affect these interactions?

3, How the non-bond interactions between the atoms from the lipid are  
calculated (e.g., the LJ and coulombic interactions)? Does the changes  
in the [atomtypes]affect these interactions?

Thank you very much for your time and your kindness. I really  
appreciate your help.

Regards

Ruo-Xu Gu