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
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
