[gmx-users] Problem in energy calculation

[Gonzalez Fernandez, Cristina]

Dear Gromacs users,





I want to calculate the van der waals and electrostatic interaction energy  between a lipid and water. For that purpose, and following the gromacs tutorials I have performed the following steps:



  *   I have include: energygrps = Other Water  in the .mdp file to be used in the energy minimization. I copy the .mdp file:



; minim.mdp - used as input into grompp to generate em.tpr
integrator    = cg        ; Algorithm (steep = steepest descent minimization)
emtol        = 1000.0      ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep          = 0.01      ; Energy step size
nsteps        = 50000          ; Maximum number of (minimization) steps to perform
energygrps      = Other Water
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist            = 1            ; Frequency to update the neighbor list and long range forces
cutoff-scheme       = Verlet
ns_type            = grid        ; Method to determine neighbor list (simple, grid)
coulombtype        = PME        ; Treatment of long range electrostatic interactions
rcoulomb        = 1.4        ; Short-range electrostatic cut-off
rvdw            = 1.4        ; Short-range Van der Waals cut-off
pbc            = xyz         ; Periodic Boundary Conditions (yes/no)





  *   From the output of the minimization (em.gro) I have grouped Other (lipid) and Water:

gmx make_ndx -f em.gro -o index.ndx

>1 | 11

>q

               and I have added energygrps = Other Water  in the .mdp file of the nvt equilibration (nvt.mdp). I copy the .mdp file





title                = Lipid   NVT equilibration
define                = -DPOSRES    ; position restrain the protein
; Run parameters
integrator          = md        ; leap-frog integrator
nsteps                = 50000        ; 2 * 50000 = 100 ps
dt                    = 0.002        ; 2 fs
; Output control
nstxout                = 500        ; save coordinates every 1.0 ps
nstvout                 = 500        ; save velocities every 1.0 ps
nstenergy           = 500        ; save energies every 1.0 ps
nstlog                = 500        ; update log file every 1.0 ps
energygrps              = Other Water
; Bond parameters
continuation            = no        ; first dynamics run
constraint_algorithm    = lincs        ; holonomic constraints
constraints            = all-bonds    ; all bonds (even heavy atom-H bonds) constrained
lincs_iter            = 1            ; accuracy of LINCS
lincs_order            = 4            ; also related to accuracy
; Nonbonded settings
cutoff-scheme           = Verlet
ns_type                = grid        ; search neighboring grid cells
nstlist                = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb            = 1.4        ; short-range electrostatic cutoff (in nm)
rvdw                = 1.4        ; short-range van der Waals cutoff (in nm)
rlist                   = 1.4
vdwtype                 = Cut-off
vdw_modifier            = Potential-shift-Verlet
; Electrostatics
coulombtype            = PME    ; Particle Mesh Ewald for long-range electrostatics
ewald-rtol              = 1e-6
pme_order            = 4        ; cubic interpolation
fourierspacing        = 0.16    ; grid spacing for FFT
coulomb_modifier        = Potential-shift-Verlet
; Temperature coupling is on
tcoupl           = V-rescale                ; modified Berendsen thermostat
tc-grps                = System    ; two coupling groups - more accurate
tau_t                = 0.1                 ; time constant, in ps
ref_t                = 298                ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl                 = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc                = xyz            ; 3-D PBC
; Dispersion correction
DispCorr            = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel                 = yes        ; assign velocities from Maxwell distribution
gen_temp            = 298        ; temperature for Maxwell distribution
gen_seed            = -1        ; generate a random seed










           Then, for the nvt equilibration, I generated the .tpr file  and run the equilibration:


           gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

           nohhup gmx mdrun -deffnm nvt &





  *   Finally, I used gmx energy to determine the electrostatic and van der waals energies. However, when I select 42 (Coul-SR: Other-Water) and 43 (LJ-SR: Other-Water) the results for both energies are 0 KJ/mol.



What am I doing wrong? Could anyone help me to obtain interaction energies different from 0?



Thank you in advance,

C.





________________________________