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
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