GROMACS version: 2018
GROMACS modification: No
Dear all,
I have performed a Steer molecular dynamics simulation, in which I fixed molecule A (named Rib in my system) and pull molecule B (Nascent in my system) away.
During the simulation, I used the PME method for long-range electrostatics, now I want to calculate electrostatic interaction between molecule A and B (both long-range and short-range so I used Reaction Field to obtain long-range interaction as this paper mention: https://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00012)
In the mdp file for interaction energy calculation:
energygrps = Rib Nascent
coulombtype = Reaction-Field
rcoulomb = 1.2
This means that the interaction of atoms in molecules Rib and molecule Nascent will be treated as short-range interaction if the distance smaller than 1.2 nm, and long-range if larger than 1.2 nm.
When I use gmx energy to calculate interaction energy I got only these options:
1 Bond 2 Angle 3 Proper-Dih. 4 Improper-Dih. 5 LJ-14 6 Coulomb-14 7 LJ-(SR) 8 Disper.-corr. 9 Coulomb-(SR) 10 Position-Rest. 11 COM-Pull-En. 12 Potential 13 Kinetic-En. 14 Total-Energy 15 Conserved-En. 16 Temperature 17 Pres.-DC 18 Pressure 19 Constr.-rmsd 20 Vir-XX 21 Vir-XY 22 Vir-XZ 23 Vir-YX 24 Vir-YY 25 Vir-YZ 26 Vir-ZX 27 Vir-ZY 28 Vir-ZZ 29 Pres-XX 30 Pres-XY 31 Pres-XZ 32 Pres-YX 33 Pres-YY 34 Pres-YZ 35 Pres-ZX 36 Pres-ZY 37 Pres-ZZ 38 #Surf*SurfTen 39 Coul-SR:Rib-Rib 40 LJ-SR:Rib-Rib 41 Coul-14:Rib-Rib 42 LJ-14:Rib-Rib 43 Coul-SR:Rib-Nascent 44 LJ-SR:Rib-Nascent 45 Coul-14:Rib-Nascent 46 LJ-14:Rib-Nascent 47 Coul-SR:Rib-rest 48 LJ-SR:Rib-rest 49 Coul-14:Rib-rest 50 LJ-14:Rib-rest 51 Coul-SR:Nascent-Nascent 52 LJ-SR:Nascent-Nascent 53 Coul-14:Nascent-Nascent 54 LJ-14:Nascent-Nascent 55 Coul-SR:Nascent-rest 56 LJ-SR:Nascent-rest 57 Coul-14:Nascent-rest 58 LJ-14:Nascent-rest 59 Coul-SR:rest-rest 60 LJ-SR:rest-rest 61 Coul-14:rest-rest 62 LJ-14:rest-rest 63 T-RNC 64 T-Water_and_ions
How can I obtain the long-range electrostatic interactions?
Best regards,