GROMACS version:2020

GROMACS modification: No

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Dear GROMACS Users,

I am simulating membrane proteins in presence of DIPC and DPPC lipids using coarse grained simulations. I performed an NPT run at 295 K temperature. The structure of the membrane proteins gets distorted by the end of simulations.

Following are the mdp file parameters:

; 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 = 0.02

nsteps = 600000000

; 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 = 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 = 25000

nstvout = 0

nstfout = 0

; Output frequency for energies to log file and energy file

nstlog = 1000

nstcalcenergy = 100

nstenergy = 10000

; Output frequency and precision for .xtc file

nstxout-compressed = 5000

compressed-x-precision = 100

; 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 =

; NEIGHBORSEARCHING PARAMETERS

; cut-off scheme (Verlet: particle based cut-offs)

cutoff-scheme = Verlet

; nblist update frequency

nstlist = 20

; 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

; long-range cut-off for switched potentials

; OPTIONS FOR ELECTROSTATICS AND VDW

; Method for doing electrostatics

coulombtype = reaction-field

coulomb-modifier = Potential-shift-Verlet

rcoulomb-switch = 0

rcoulomb = 1.2

; Relative dielectric constant for the medium and the reaction field

epsilon_r = 15

epsilon_rf = 0

; Method for doing Van der Waals

vdw_type = cutoff

vdw-modifier = Potential-shift-verlet

; cut-off lengths

rvdw-switch = 0

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-05

ewald-rtol-lj = 0.001

lj-pme-comb-rule = Geometric

ewald-geometry = 3d

epsilon-surface = 0

implicit-solvent = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS

; Temperature coupling

tcoupl = v-rescale

nsttcouple = -1

nh-chain-length = 10

print-nose-hoover-chain-variables = no

; Groups to couple separately

tc-grps = DPPC W WF ION CHOL DIPC Protein

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

tau_t = 1.0 1.0 1.0 1.0 1.0 1.0 1.0

ref_t = 295 295 295 295 295 295 295

; pressure coupling

Pcoupl = parrinello-rahman

Pcoupltype = semiisotropic

nstpcouple = -1

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

tau_p = 12.0

compressibility = 3e-4 3e-4 3e-4 3e-4 3e-4 3e-4 3e-4

ref_p = 1.0 1.0 1.0 1.0 1.0 1.0 1.0

; 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

; 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 = 295

gen_seed = 473529

; 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

; 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 = -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

; 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

Any help of suggestions will be appreciated.

Thanks and regards,