[gmx-users] gromacs electrostatic energy

[王珍]

Hi all, I use two methods to calculate the electrostatic energy of two atoms of RNA. 
Firstly, when I use the g_enengy to calculate the electrostatic energy in gromacs. 
Secondly, I just use the formula of electrostatic energy (E=f*q(i)*q(j)/r), 
The results of two methods make a great difference. For gromacs, the algorithm of electrostatic energy is not the (E=f*q(i)*q(j)/r) ?

Thank you very much.

The following is the file of mdp.
title               =  1ZIH
cpp                 =  /lib/cpp 

;run parameters 
integrator          =  md
dt                  =  0.002                    ; ps 
nsteps              =  2                ; total 1ns
nstcomm             =  100
define              = -DPOSRES

;output control
nstxout             =  1000                     ; collect data every 2 ps
nstxtcout           =  1000
nstvout             =  1000
nstfout             =  0
nstlog              =  1000
nstcalcenergy       =  1                     ;frequency fo calculating the energy
nstenergy           =  1000                    ;frequency to write energies to energy file

;Bond parameter
continuation           = yes                     ;restarting after NPT
constraint-algorithm   = lincs 
constraints            = all-bonds               ;none
lincs_iter             = 1
lincs_order            = 4

;Neighborsearching 
ns_type             =  grid
nstlist             =  10
rlist               =  1.0
rcoulomb            =  1.0
vdwtype             =  cut-off
rvdw                =  1.0

;Electrostatics 
coulombtype         =  PME
pme_order      =  4
fourierspacing      =  0.12  
                     
;Temperature coupling is on 
Tcoupl              = V-rescale                     ;berendsen
tc-grps             = system  
Tau_t               = 0.1   
ref_t               = 300         
   
; Berendsen Pressure coupling is on
Pcoupl              = Parrinello-Rahman
Pcoupltype          = isotropic
tau_p               =  0.5       
compressibility     =  4.5e-05
ref_p               =  1.0  

;Periodic boundary conditions
pbc                 = xyz

;Dispersion correction
DispCorr            = EnerPres
refcoord_scaling    = all
; Generate velocites 
gen_vel             =  no

energygrps = a115 a17