GROMACS version: 2023.0-gcc11.2.0-mkl-cuda

GROMACS modification: Yes/No

Hi everybody,

I am experiencing troubles with lipid bilayers and lipid/protein systems using gmx 2023.

in pure charmm36 bilayer simulations of E coli PLE I have well exercised before in gmx2016, vacuum bubbles arise between the lipid tails from the two membrane leaflets. correspondingly the area per lipids is larger than in our paper, and in new test simulations I have done on the same HPC now using gmx 2016 and 2020. the potential energy at t=0 is more or less identical. I am using identical pressure couplings, verlet and switch setups etc.

here the area per lipid (average from 100-200ns) at 296K

gmx2016|paper| 63.33±0.15 Å^2 (sd over 3 replica simulations and 100ns intervals)

gmx2016 63.46

gmx2020 63.54

gmx2023 66.48

and here the mdp file

; Created by:

; :-) GROMACS - gmx grompp, 2023 (-:

;

; Executable: /apps/SPACK/0.19.1/opt/linux-almalinux8-zen2/gcc-11.2.0/gromacs-2023-z4x4kdhoxzz4r6snx4jvfnxcwtjvsar7/bin/gmx

; Data prefix: /apps/SPACK/0.19.1/opt/linux-almalinux8-zen2/gcc-11.2.0/gromacs-2023-z4x4kdhoxzz4r6snx4jvfnxcwtjvsar7

; Working dir: /home/atuin/a101cb/a101cb10/gasderminD/10DSF_avanti/04_MD296K_noDSF

; Command line:

; gmx grompp -f md.mdp -p …/04_MD296K_noverlet_noDSF/topol_avanti.top -c …/04_MD296K_noverlet_noDSF/formd.pdb -n …/04_MD296K_noverlet_noDSF/index.ndx -maxwarn 1

; 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 =

; RUN CONTROL PARAMETERS

integrator = md

; Start time and timestep in ps

tinit = 0

dt = 0.002

nsteps = 100000000

; 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

; Multiple time-stepping

mts = no

; 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 = System

; LANGEVIN DYNAMICS OPTIONS

; Friction coefficient (amu/ps) and random seed

bd-fric = 0

ld-seed = 1983

; ENERGY MINIMIZATION OPTIONS

; Force tolerance and initial step-size

emtol = 10

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 = 00000

nstvout = 00000

nstfout = 0

; Output frequency for energies to log file and energy file

nstlog = 50000

nstcalcenergy = 100

nstenergy = 50000

; Output frequency and precision for .xtc file

nstxout-compressed = 50000

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)

cutoff-scheme = Verlet

; nblist update frequency

nstlist = 10

; Periodic boundary conditions: xyz, no, xy

pbc = xyz

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 = 1.2

; long-range cut-off for switched potentials

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = PME

coulomb-modifier = Potential-shift-Verlet

rcoulomb-switch = 0

rcoulomb = 1.2

; Relative dielectric constant for the medium and the reaction field

epsilon-r = 1

epsilon_rf = 1

; Method for doing Van der Waals

vdw-type = cut-off

vdw-modifier = Force-switch

; cut-off lengths

rvdw-switch = 0.8

rvdw = 1.2

; 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-5

ewald-rtol-lj = 0.001

lj-pme-comb-rule = Geometric

ewald_geometry = 3d

epsilon_surface = 0

implicit_solvent = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS

ensemble-temperature-setting = auto

ensemble-temperature = -1

; Temperature coupling

tcoupl = Nose-Hoover

nsttcouple = -1

nh-chain-length = 1

print-nose-hoover-chain-variables = no

; Groups to couple separately

tc-grps = Membrane Water_and_ions

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

tau-t = 0.5 0.5

ref-t = 296 296

; pressure coupling

Pcoupl = Parrinello-Rahman

Pcoupltype = semiisotropic

nstpcouple = -1

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

tau-p = 5.0

compressibility = 4.5e-5 4.5e-5

ref-p = 1.0 1.0

; Scaling of reference coordinates, No, All or COM

refcoord-scaling = No

; OPTIONS FOR QMMM calculations

QMMM = no

; Groups treated with MiMiC

QMMM-grps =

; SIMULATED ANNEALING

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

annealing = no

; 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 = yes

gen-temp = 290

gen-seed = -973078537

; OPTIONS FOR BONDS

constraints = h-bonds

; 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 = 1e-04

; 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 = 6

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

; rotates over more degrees than

lincs-warnangle = 60

; 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

; AWH biasing

awh = 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 = 0

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-function = beutler

sc-alpha = 0

sc-power = 1

sc-r-power = 6

sc-sigma = 0.3

sc-coul = no

sc-gapsys-scale-linpoint-lj = 0.85

sc-gapsys-scale-linpoint-q = 0.3

sc-gapsys-sigma-lj = 0.3

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

; 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

; Electric fields

; Format for electric-field-x, etc. is: four real variables:

; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),

; and sigma (ps) width of the pulse. Omega = 0 means static field,

; sigma = 0 means no pulse, leaving the field to be a cosine function.

electric-field-x = 0 0 0 0

electric-field-y = 0 0 0 0

electric-field-z = 0 0 0 0

; Density guided simulation

density-guided-simulation-active = false

; QM/MM with CP2K

qmmm-cp2k-active = false