Fatal error: Requested Parrinello-Rahman barostat with md-vv

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1

GROMACS version: 2021.3gpu
GROMACS modification: No
Hi everyone, I am trying to set up the simulation of protein dimer in solvent using md-vv integrator, Nosé-Hoover chains termostat and Parinello-Rahman barostat. I get following Fatal error:

Requested Parrinello-Rahman barostat with md-vv. This combination is only
available in the modular simulator. Some other selected options are, however,
only available in the legacy simulator. Use a different pressure control
algorithm.

I get that some mdp options are causing this, but I have no idea which ones. Here is my input mdp file:

; Run parameters

integrator = md-vv ; velocity verlet

nsteps = 50000000 ; 2 * 50000000 = 100000 ps (100 ns)
dt = 0.002 ; 2 fs

; Output control

nstxout = 50000 ; suppress bulky .trr file by specifying
nstvout = 50000 ; 0 for output frequency of nstxout,
nstfout = 50000 ; nstvout, and nstfout
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 50000 ; update log file every 100.0 ps
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system

; Bond parameters

continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy

; Neighborsearching

cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rlist = 1.2

; Electrostatics

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
vdwtype = cutoff
vdw-modifier = force-switch
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
rvdw-switch = 1.0

; Temperature coupling is on

tcoupl = nose-hoover
nsttcouple = 1
nh-chain-length = 10
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.5 0.5 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K

; Pressure coupling is on

pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1

; Periodic boundary conditions

pbc = xyz ; 3-D PBC

; Dispersion correction

DispCorr = no ; account for cut-off vdW scheme

; Velocity generation

gen_vel = no ; Velocity generation is off

I will be very grateful for your help to overcome this issue.

2

Hi,
the error suggests to change the pressure control algorithm, that is defined by the pcoupl = option in mdp file.
You can use Martyna-Tuckerman-Tobias-Klein implementation in place of Parrinello-Rahman.

See here more on velocity-verlet integrator Molecular Dynamics — GROMACS 2022.3 documentation

here on barostat implementation Molecular Dynamics — GROMACS 2022.3 documentation

here on mdp option Molecular dynamics parameters (.mdp options) — GROMACS 2022.3 documentation

I hope it helps
\Alessandra