[gmx-users] Problem to compute interaction energy between different groups

[ARNAB MUKHERJEE]

Hello,

I have simulated a system of DNA and Protamine (Coarse grained, Martini). I
want to look at the interaction energy between different groups like DNA -
Protamine, DNA - ions, etc. I have defined energy groups in the mdp file,
and I pass the index file with the groups while building the tpr file.
After the run is complete, when I run gmx energy command, no matter what
interaction energy I choose, it always gives me 0 (for all time steps). But
the total Potential energy works. I am not able to understand why?

This is how my .mdp file looks like :

title           = NVT equilibration with position restraint on all solute
(topology modified)
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 60000000      ; 1 * 500000 = 500 ps
;nsteps          = 5000
dt              = 0.01          ; 1 fs
; Output control
nstxout         = 0     ; save coordinates every 10 ps
nstvout         = 0     ; save velocities every 10 ps
nstcalcenergy   = 50
nstenergy       = 1000  ; save energies every 1 ps
nstxtcout       = 2500
;nstxout-compressed  = 5000   ; save compressed coordinates every 1.0 ps
                             ; nstxout-compressed replaces nstxtcout
;compressed-x-grps  = System  ; replaces xtc-grps
nstlog          = 1000  ; update log file every 1 ps
; Bond parameters
continuation    = no   ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints     = none          ; all bonds (even heavy atom-H bonds)
constrained
;lincs_iter     = 2                         ; accuracy of LINCS
lincs_order     = 4                         ; also related to accuracy
epsilon_r       = 15
; Neighborsearching
cutoff-scheme   = Verlet
ns_type         = grid          ; search neighboring grid cels
nstlist         = 10            ; 20 fs
rvdw_switch     = 1.0
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
vdwtype         = Cut-off       ; Twin range cut-offs rvdw >= rlist
;vdw-modifier    = Force-switch
;Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4                 ; cubic interpolation
fourierspacing  = 0.12          ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = v-rescale
tc_grps         = System
tau_t           = 1.0
ref_t           = 300

energygrps = DNA Protein W ION

freezegrps = DNA
freezedim = Y Y Y

; Pressure coupling is off
pcoupl          = no            ; no pressure coupling in NVT
; Periodic boundary conditions
pbc             = xyz           ; 3-D PBC
; Dispersion correctiion
DispCorr        = no            ; account for cut-off vdW scheme
; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell
distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm         = 50
comm-mode       = Linear
comm-grps       = System
;
refcoord_scaling = com


I would greatly appreciate any help.

Thanks in advance,

Thanks and Regards,

Arnab Mukherjee