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

[chris.neale at utoronto.ca]

Your first question is addressed in the following document:

http://www.pomeslab.com/files/lipidCombinationRules.pdf

Your second and third question are addressed (in general form) in the  
gromacs manual.

If you want a topology file, send me a personal email indicating the  
lipid that you are using (no other questions by personal email though  
please).

Chris.

-- original message --

Dear All:

I am using GROMACS package to simulate membrane proteins. I plan to =20
use Berger's united atom force field (Berger's UA FF) for lipids and =20
OPLS_AA force field (OPLS_AA FF) for proteins.

I have read the guide post kindly by Prof. Dr. Chris Neale in previous =20
mailing lists very carefully. According to his guide, the following =20
steps are needed:

1). Added [atomtypes] from lipid.itp to ffoplsaanb.itp -- after =20
changing c6/c12
to sigma/epsilon. Also added atomtype H from olsa_369 to match H expected by
pope.itp
    - sigma   =3D (c12/c6)^1/6
    - epsilon =3D c6/(4*sigma^6)

2). Added [pairtypes] from lipid.itp to ffoplsaanb.itp -- after =20
changing c6/c12
to sigma/epsilon. (gives effective fudgeLJ of 0.125). Also changed all =20
reference
to OW to opls_116 (opls spc water oxygen) and simply removed any with =20
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 the=
se
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 =20
and scale Coulombic1-4 interaction by 1.0. OPLS_AA FF scale both of =20
them by 0.5, right? From the above changes, I find that the changes of =20
the sigma or epsilon (or c6 and c12) is only associate with the LJ1-4 =20
interaction. So, how the Coulombic1-4 interaction is scaled properly? =20
Do I need additional changes?

2, the non-bond interactions between the atoms from the lipid and the =20
atoms from the protein are need to be calculated, right?  My question =20
is how these interactions are calculated? Does the changes in the =20
[atomtypes]affect these interactions?

3, How the non-bond interactions between the atoms from the lipid are =20
calculated (e.g., the LJ and coulombic interactions)? Does the changes =20
in the [atomtypes]affect these interactions?

Thank you very much for your time and your kindness. I really =20
appreciate your help.

Regards

Ruo-Xu Gu