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