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.
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