Gromacs velocity autocorrelation function

User discussions
1

GROMACS version:2024.2
GROMACS modification: No
I am trying to study the structure and dynamics of glycerol in water using opls aa force field while calculating velocity auto correlation function using gmx velacc for o in water and o in glycerol but both are zero all the way here is my production run and equilibrium run mdp file

eq.mdp
;PREPROCESSING parameters
cpp = /lib/cpp
integrator = md
dt = 0.002
nsteps = 50000000 ;100 ns
nstcomm = 1

;OUPUT CONTROL parameters.
nstxout = 500
nstvout = 500
nstfout = 500
nstlog = 500
nstenergy = 500
nstxtcout = 500
energygrps = system
;NEIGHBOUR SEARCHING parameters.
nstlist = 10
ns_type = grid
rlist = 1.0
;ELECTROSTATIC and VdW parameters.
vdwtype = cut-off
coulombtype = PME ; Particle Mesh Ewald for long-range
fourierspacing = 0.12 ; grid spacing for FFT
pme-order = 4
ewald-rtol = 1e-05
rcoulomb = 1.0
rvdw = 1.0
epsilon-r = 1.0
;BERENDSEN TEMPERATURE COUPLING is on in two groups
Tcoupl = v-rescale
tc-grps = system
tau_t = 0.01
ref_t = 300
;PRESSURE COUPLING is on
Pcoupl = berendsen
tau_p = 0.8
compressibility = 4.6e-5
ref_p = 1.0
;SIMULATED ANNEALING parameters are not specified.
;GENERATE VELOCITIES is on at 310K
gen_vel = yes ; generate initially
gen_temp = 300
gen_seed = 173529 ;give different values for different trials.
ld_seed = 1993
;BONDS parameters
constraints = all-bonds
constraint-algorithm = LINCS
unconstrained-start = no
pbc = xyz
##############
production.mdp

;PREPROCESSING parameters
tinit = 0
integrator = md
dt = 0.002
nsteps = 100000000 ;200 ns
nstcomm = 1

;OUPUT CONTROL parameters.
nstxout = 1000
nstvout = 1000
nstfout = 1000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
energygrps = system
;NEIGHBOUR SEARCHING parameters.
nstlist = 10
ns_type = grid
rlist = 1.0
;ELECTROSTATIC and VdW parameters.
vdwtype = cut-off
coulombtype = PME
fourierspacing = 0.12 ; grid spacing for FFT
pme-order = 4
ewald-rtol = 1e-05
rcoulomb = 1.0
rvdw = 1.0
epsilon-r = 1.0
;BERENDSEN TEMPERATURE COUPLING is on in two groups
Tcoupl = v-rescale
tc-grps = system
tau_t = 0.01
ref_t = 300

;PRESSURE COUPLING is on
Pcoupl = no
;SIMULATED ANNEALING parameters are not specified.
;GENERATE VELOCITIES is on at 310K
gen_vel = no; ; generate initially
gen_temp = 300
gen_seed = 173529 ;give different values for different trials.
ld_seed = 1993
;BONDS parameters
constraints = all-bonds
constraint-algorithm = LINCS
unconstrained-start = yes
pbc = xyz
;SIMULATED ANNEALING parameters are not specified.

2

What is the temperature/kinetic energy over time? I feel like setting tau_t = 0.01 to such a small value might just destroy all the correlation as you couple with the thermostat all the time and the stochastic term in the v-rescale will delete all type of correlation (e.g. auto-correlation functions at zero), albeit I might be very wrong here.