GROMACS version: 2020

GROMACS modification: No

I am a newbie with Gromacs and following an example script found in this tutorial I fail to reproduce the minimization step in vacuum without PBC. The failure coming from the fact that the script is deprecated when used with gromacs 2020. Here is the contents of the script:

;

; File ‘mdout.mdp’ was generated

; By user: alex (22065)

; On host: md02

; At date: Thu Mar 23 09:13:15 2017;

; Created by:

; :-) GROMACS - gmx grompp, 2016.1 (-:

;

; Executable: /usr/local/gromacs-2016.1/bin/gmx

; Data prefix: /usr/local/gromacs-2016.1

; Working dir: /coarse/alex/TUTORIALS/pepmd-v5/md-tutorial

; Command line:

; gmx grompp -p protein.top -c protein.gro -f minim.mdp -o protein-EM-vacuum.tpr; VARIOUS PREPROCESSING OPTIONS

; Preprocessor information: use cpp syntax.

; e.g.: -I/home/joe/doe -I/home/mary/roe

include =

; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)

define = -DFLEXIBLE; RUN CONTROL PARAMETERS

integrator = steep

; Start time and timestep in ps

tinit = 0

dt = 0.001

nsteps = 500

; For exact run continuation or redoing part of a run

init-step = 0

; Part index is updated automatically on checkpointing (keeps files separate)

simulation-part = 1

; mode for center of mass motion removal

comm-mode = Linear

; number of steps for center of mass motion removal

nstcomm = 100

; group(s) for center of mass motion removal

comm-grps =; LANGEVIN DYNAMICS OPTIONS

; Friction coefficient (amu/ps) and random seed

bd-fric = 0

ld-seed = -1; ENERGY MINIMIZATION OPTIONS

; Force tolerance and initial step-size

emtol = 1.0

emstep = 0.01

; Max number of iterations in relax-shells

niter = 20

; Step size (ps^2) for minimization of flexible constraints

fcstep = 0

; Frequency of steepest descents steps when doing CG

nstcgsteep = 1000

nbfgscorr = 10; TEST PARTICLE INSERTION OPTIONS

rtpi = 0.05; OUTPUT CONTROL OPTIONS

; Output frequency for coords (x), velocities (v) and forces (f)

nstxout = 0

nstvout = 0

nstfout = 0

; Output frequency for energies to log file and energy file

nstlog = 1000

nstcalcenergy = 100

nstenergy = 1

; Output frequency and precision for .xtc file

nstxout-compressed = 0

compressed-x-precision = 1000

; This selects the subset of atoms for the compressed

; trajectory file. You can select multiple groups. By

; default, all atoms will be written.

compressed-x-grps =

; Selection of energy groups

energygrps = System; NEIGHBORSEARCHING PARAMETERS

; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)

cutoff-scheme = Group

; nblist update frequency

nstlist = 10

; ns algorithm (simple or grid)

ns_type = simple

; Periodic boundary conditions: xyz, no, xy

pbc = no

periodic-molecules = no

; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,

; a value of -1 means: use rlist

verlet-buffer-tolerance = 0.005

; nblist cut-off

rlist = 1

; long-range cut-off for switched potentials; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = cut-off

coulomb-modifier = Potential-shift-Verlet

rcoulomb-switch = 0

rcoulomb = 1.0

; Relative dielectric constant for the medium and the reaction field

epsilon-r = 1

epsilon-rf = 0

; Method for doing Van der Waals

vdw-type = Cut-off

vdw-modifier = Potential-shift-Verlet

; cut-off lengths

rvdw-switch = 0

rvdw = 1.0

; Apply long range dispersion corrections for Energy and Pressure

DispCorr = No

; Extension of the potential lookup tables beyond the cut-off

table-extension = 1

; Separate tables between energy group pairs

energygrp-table =

; Spacing for the PME/PPPM FFT grid

fourierspacing = 0.12

; FFT grid size, when a value is 0 fourierspacing will be used

fourier-nx = 0

fourier-ny = 0

fourier-nz = 0

; EWALD/PME/PPPM parameters

pme-order = 4

ewald-rtol = 1e-05

ewald-rtol-lj = 0.001

lj-pme-comb-rule = Geometric

ewald-geometry = 3d

epsilon-surface = 0; IMPLICIT SOLVENT ALGORITHM

implicit-solvent = No; GENERALIZED BORN ELECTROSTATICS

; Algorithm for calculating Born radii

gb-algorithm = Still

; Frequency of calculating the Born radii inside rlist

nstgbradii = 1

; Cutoff for Born radii calculation; the contribution from atoms

; between rlist and rgbradii is updated every nstlist steps

rgbradii = 1

; Dielectric coefficient of the implicit solvent

gb-epsilon-solvent = 80

; Salt concentration in M for Generalized Born models

gb-saltconc = 0

; Scaling factors used in the OBC GB model. Default values are OBC(II)

gb-obc-alpha = 1

gb-obc-beta = 0.8

gb-obc-gamma = 4.85

gb-dielectric-offset = 0.009

sa-algorithm = Ace-approximation

; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA

; The value -1 will set default value for Still/HCT/OBC GB-models.

sa-surface-tension = -1; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling

tcoupl = No

nsttcouple = -1

nh-chain-length = 10

print-nose-hoover-chain-variables = no

; Groups to couple separately

tc-grps =

; Time constant (ps) and reference temperature (K)

tau-t =

ref-t =

; pressure coupling

pcoupl = No

pcoupltype = Isotropic

nstpcouple = -1

; Time constant (ps), compressibility (1/bar) and reference P (bar)

tau-p = 1

compressibility =

ref-p =

; Scaling of reference coordinates, No, All or COM

refcoord-scaling = No; OPTIONS FOR QMMM calculations

QMMM = no

; Groups treated Quantum Mechanically

QMMM-grps =

; QM method

QMmethod =

; QMMM scheme

QMMMscheme = normal

; QM basisset

QMbasis =

; QM charge

QMcharge =

; QM multiplicity

QMmult =

; Surface Hopping

SH =

; CAS space options

CASorbitals =

CASelectrons =

SAon =

SAoff =

SAsteps =

; Scale factor for MM charges

MMChargeScaleFactor = 1

; Optimization of QM subsystem

bOPT =

bTS =; SIMULATED ANNEALING

; Type of annealing for each temperature group (no/single/periodic)

annealing =

; Number of time points to use for specifying annealing in each group

annealing-npoints =

; List of times at the annealing points for each group

annealing-time =

; Temp. at each annealing point, for each group.

annealing-temp =; GENERATE VELOCITIES FOR STARTUP RUN

gen-vel = no

gen-temp = 300

gen-seed = -1; OPTIONS FOR BONDS

constraints = none

; Type of constraint algorithm

constraint-algorithm = Lincs

; Do not constrain the start configuration

continuation = no

; Use successive overrelaxation to reduce the number of shake iterations

Shake-SOR = no

; Relative tolerance of shake

shake-tol = 0.0001

; Highest order in the expansion of the constraint coupling matrix

lincs-order = 4

; Number of iterations in the final step of LINCS. 1 is fine for

; normal simulations, but use 2 to conserve energy in NVE runs.

; For energy minimization with constraints it should be 4 to 8.

lincs-iter = 1

; Lincs will write a warning to the stderr if in one step a bond

; rotates over more degrees than

lincs-warnangle = 30

; Convert harmonic bonds to morse potentials

morse = no; ENERGY GROUP EXCLUSIONS

; Pairs of energy groups for which all non-bonded interactions are excluded

energygrp-excl =; WALLS

; Number of walls, type, atom types, densities and box-z scale factor for Ewald

nwall = 0

wall-type = 9-3

wall-r-linpot = -1

wall-atomtype =

wall-density =

wall-ewald-zfac = 3; COM PULLING

pull = no; ENFORCED ROTATION

; Enforced rotation: No or Yes

rotation = no; Group to display and/or manipulate in interactive MD session

IMD-group =; NMR refinement stuff

; Distance restraints type: No, Simple or Ensemble

disre = No

; Force weighting of pairs in one distance restraint: Conservative or Equal

disre-weighting = Conservative

; Use sqrt of the time averaged times the instantaneous violation

disre-mixed = no

disre-fc = 1000

disre-tau = 0

; Output frequency for pair distances to energy file

nstdisreout = 100

; Orientation restraints: No or Yes

orire = no

; Orientation restraints force constant and tau for time averaging

orire-fc = 0

orire-tau = 0

orire-fitgrp =

; Output frequency for trace(SD) and S to energy file

nstorireout = 100; Free energy variables

free-energy = no

couple-moltype =

couple-lambda0 = vdw-q

couple-lambda1 = vdw-q

couple-intramol = no

init-lambda = -1

init-lambda-state = -1

delta-lambda = 0

nstdhdl = 50

fep-lambdas =

mass-lambdas =

coul-lambdas =

vdw-lambdas =

bonded-lambdas =

restraint-lambdas =

temperature-lambdas =

calc-lambda-neighbors = 1

init-lambda-weights =

dhdl-print-energy = no

sc-alpha = 0

sc-power = 1

sc-r-power = 6

sc-sigma = 0.3

sc-coul = no

separate-dhdl-file = yes

dhdl-derivatives = yes

dh_hist_size = 0

dh_hist_spacing = 0.1; Non-equilibrium MD stuff

acc-grps =

accelerate =

freezegrps =

freezedim =

cos-acceleration = 0

deform =; simulated tempering variables

simulated-tempering = no

simulated-tempering-scaling = geometric

sim-temp-low = 300

sim-temp-high = 300; Electric fields

; Format is number of terms (int) and for all terms an amplitude (real)

; and a phase angle (real)

E-x =

; Time dependent (pulsed) electric field. Format is omega, time for pulse

; peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving

; the field to be a cosine function.

E-xt =

E-y =

E-yt =

E-z =

E-zt =; Ion/water position swapping for computational electrophysiology setups

; Swap positions along direction: no, X, Y, Z

swapcoords = no

adress = no; User defined thingies

user1-grps =

user2-grps =

userint1 = 0

userint2 = 0

userint3 = 0

userint4 = 0

userreal1 = 0

userreal2 = 0

userreal3 = 0

userreal4 = 0

running that script triggers an error about deprecated Group value for cutoff-scheme option. When trying to switch cutoff-scheme from Group to Verlet, I get another error telling that Verlet option must be used with pbc option set to either xyz or xy. However, I want to perform this first minimization step in vacuum before generating any solvation box. Would you know how to make this script work with gromcas 2020 ?

thanks a lot

Eric