[gmx-users] LJ14 interactions on DPPC

[David L. Bostick]

> 1 In the [pairs] section, from my understanding, there should be more
> 1-4 interactions in DPPC molecules.  Why is it not all listed?

All 1-4 interactions should be listed in the [pairs] section except for the
tails, which are treated with the dihedral RB potential.

> 2 Does LJ14 in DPPC always be zero, that is all the energy term has
> already been taking into account by [dihedrals]?

Correct, for the tails, the 1-4 interaction should be zero. This is how the
potential was parameterized.

> 3 If using Dr. Tieleman's files, whether gen-pairs = yes or no, will
> there  always be values for C6 and C12 for LJ14 because of the [pairs]
> and [pairtypes] listed?

If you set genpairs=yes, and the 1-4 interactions are listed in [pairs] the
LJ interactions will be calculated for those pairs based upon fudgeLJ and
fudgeQQ. If genpairs=no, the 1-4 interactions will be taken from the
[pairtypes] section of the topology file(s). I believe Tieleman's files
include the pairlist, so you should use whatever those files dictate to
remain consistent.


David B.

>
> Any help in this matter would be greatly appreciated.
>
> Sukit
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>