[gmx-users] Bonds between P and O in bilayer head groups

[Mijiddorj Batsaikhan]

Dear gmx users,

I want to simulate membranes system using gromacs v5. Initial structure was
built by Charmm-gui. Head groups' bonds between two O- and P are single in
the Charmm topology file as a following:

ATOM H11B HAL2    0.09 !                      alpha4
ATOM P    PL      1.50 !        (-) O13  O12
ATOM O13  O2L    -0.78 !              \ /      alpha3
ATOM O14  O2L    -0.78 !               P (+)
ATOM O12  OSLP  -0.57 !              / \      alpha2
ATOM O11  OSLP   -0.57 !   (-) O14  O11
ATOM C1   CTL2   -0.08 !                 |     alpha1
ATOM HA   HAL2    0.09 !            HA---C1---HB
ATOM HB   HAL2    0.09 !                 |     theta1

One of the them is double bond in the nomenclatures.

(1) Which one is preferable for the simulation?

(2) Are some metal ions needed near the head groups for the simulation?



Best regards,

Mijiddorj