# Gromacs velocity autocorrelation function

**URL:** <https://gromacs.bioexcel.eu/t/gromacs-velocity-autocorrelation-function/11693>\
**Category:** User discussions\
**Created:** [March 6, 2025, 4:18pm UTC](https://gromacs.bioexcel.eu/t/gromacs-velocity-autocorrelation-function/11693 "2025-03-06T16:18:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![bishnu](https://avatars.discourse-cdn.com/v4/letter/b/43a26b/32.png) [@bishnu](https://gromacs.bioexcel.eu/u/bishnu)\
**Post date:** [March 6, 2025, 4:18pm UTC](https://gromacs.bioexcel.eu/t/gromacs-velocity-autocorrelation-function/11693/1 "2025-03-06T16:18:51Z")

</div>

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.

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<div class="post-metadata">

**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [March 6, 2025, 6:40pm UTC](https://gromacs.bioexcel.eu/t/gromacs-velocity-autocorrelation-function/11693/2 "2025-03-06T18:40:27Z")

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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.