# Bulk viscosity calculation using gmx **URL:** \ **Category:** User discussions\ **Created:** [May 22, 2023, 12:51pm UTC](https://gromacs.bioexcel.eu/t/bulk-viscosity-calculation-using-gmx/6464 "2023-05-22T12:51:38Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![sancharitanni](https://avatars.discourse-cdn.com/v4/letter/s/e36b37/32.png) [@sancharitanni](https://gromacs.bioexcel.eu/u/sancharitanni)\ **Post date:** [May 22, 2023, 12:51pm UTC](https://gromacs.bioexcel.eu/t/bulk-viscosity-calculation-using-gmx/6464/1 "2023-05-22T12:51:38Z")
GROMACS version: GROMACS modification: Yes/No module load gromacs/2021.5-gcc/9.5.0-mpi-openmp-cu11\_1 I have been trying to calculate bulk viscosity using Einstein relation below is my vis.mdp file.when I am trying to gmx\_mpi energy -f vis.edr -vis viscosity.xvg ,it asked me about the Opened vis.edr as single precision energy file Enter the box volume (nm^3): 9 Afterthat,I can see only two files generates evisco.xvg,eviscoi.xvg.I didnt see any viscosity value.I donot know Whether I am using the correct procedure to calculate bulk viscosity.Anyone having any idea to calculate bulk viscosity in gromacs? ; very basics of the simulation integrator = md ; solve newtown’s equation of motion dt = 0.002 ; integration time step / ps nsteps = 50000000 ; number of steps (50000000 \* 0.002 = 100 ns) ; remove drifts of the center of mass comm-mode = linear ; remove COM translation nstcomm = 10 ; number of steps for COM removal comm-grps = System ; COM translation removed from system ; control frequency of output nstvout = 0 ; write velocities to trajectory file every number of steps nstfout = 0 ; write forces to trajectory file every number of steps nstlog = 10000 ; update log file every number of steps nstcalcenergy = 10 ; calculate energies/pressures every nstenergy steps nstenergy = 10 ; write energies to energy file every number of steps nstxout-compressed = 10000 ; write positions using compression (saves memory, worse quality) compressed-x-precision = 1000 ; precision to write compressed trajectory ; next neighbor search and periodic boundary conditions nstlist = 20 ; freq. to update neighbor list & long range forces (\>= 20 w/ GPUs) rlist = 1.4 ; short-range neighbor list cutoff (nm) cutoff-scheme = Verlet ; atom-based neighbor search with an implicit buffer region pbc = xyz ; periodicity in x, y and z ; coulomb interaction coulombtype = PME ; particle-mesh ewald summation for long range (\>rcoulomb) rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) (with PME,rcoulomb \>= rvdw) coulomb-modifier = Potential-shift-Verlet ; shifts potential by constant so potential is 0 at cut-off fourierspacing = 0.168 ; spacing of FFT in reciprocal space in PME long range treatment (in nm) pme-order = 4 ; cubic PME interpolation order ; lennard-jones potential handling vdwtype = cutoff ; simple truncation cutoff vdw-modifier = Potential-shift-Verlet ; shifts potential by constant so potential is 0 at cut-off rvdw = 1.4 ; short-range vdw cutoff (in nm) DispCorr = EnerPres ; long range correction for energy and pressure from using vdw cutoff ; temperature coupling tcoupl = v-rescale ; the algorithm to use, v-rescale generates correct canonical ensemble tc-grps = System ; groups to couple to temperature bath tau-t = 1.0 ; time constant (in ps), meaning varies by algorithm ref-t = 328 ; temperature for coupling (K) nsttcouple = 1 ; frequency to couple temperature ; velocity generation gen-vel = yes ; generate velocities according to Maxwell distr. (no for initial vel 0) gen-temp = 328 ; temperature for Maxwell distribution (K) gen-seed = -1 ; generate a random seed ; pressure coupling pcoupl = no ; the algorithm to use (no for NVT) ; constraints constraints = h-bonds ; constrains bonds only involving hydrogen constraint\_algorithm = lincs ; algorithm to use, lincs should NOT be used for angle constraining lincs-order = 4 ; highest order in constraint coupling matrix expansion lincs-iter = 1 ; accuracy of lincs algorithm continuation = no ; no for applying constraints at start of run