example.inp

# specify workdir
workdir THIS_IS_A_TEST

# base values for atomtypes 
$atomtypes
# type -- 'standard' is the only one available so far
standard 
# basic atomtypes
# name            c6              c12     cs6    cs12
AR     6.2647225e-03    9.8470440e-06     0.0     0.0
$end

# specify the topologies of the molecules
$molecules
# names of the molecules
names argon       
# Topology (itp) files.
# These files must contain only the [ atoms ], [ bonds ], [ angles ], [ dihedrals ], [ pairs ] and [ exclusions ] blocks.
# Do not link to the force-field files---these links will be generated automatically by gridmaker based on the $atomtypes and $variations.
itp   argon.itp   
$end

# Variations
$variation
# the name of the variation; the fundamental variation MUST be named `main'.
name        main
# parameters defining the variation, following the syntax ATOMTYPE/PARAMETER.
pars        AR/c6        AR/c12
# type of variation---you will most likely use `cartesian'
type        cartesian
# starting values for each parameter
start       5.929722500000000722e-03 9.147044000000001052e-06
# step values for each parameter
step        0.005e-03      0.005e-06
# sizes along each dimension
size        51            51
$end

$gridshift
maxshifts   10
#           min[0]  max[0]  min[1]  max[1]  min[2]  max[2]  ...  min[dim]  max[dim]
margins     0.25    0.75    0.25    0.75
# The CG of the `ncut'-times-the-size-of-the-grid best points are checked against the margins.
ncut        0.0005
# Keep points from previous grids; you should use `yes' in all cases except interpolation.
keepsamples no
$end

$grid
# reweight types
reweight standard_force
labels $C_6$ $C_12$
# samples based on linear index
samples 0 50 650 675 1300 1925 1950 2550 2600
# for all grids, always use the same samples listed above
fixsamples yes
$end

$subgrid
method linear
# factors along dimensions 
factors 4 4
$end

# Protocols.
$protocol
type liquid
name liq
mdps em_pme.mdp nvt_pme.mdp npt_pme.mdp md_pme.mdp
molecule argon
coords argon.gro
length 5.00
nmols 1500
$end

# $protocol
# type gas
# name gas
# molecule argon
# mdps mdp/argon/em_gas.mdp mdp/argon/sd_gas.mdp
# coords argon.gro
# gasdipole 1.85
# # infinite polarizability ==> correction == NULL
# polarizability 1e+23
# $end

$protocol
type slab
name slab
#nprocs 16
mdps em_slab.mdp nvt_slab.mdp md_slab.mdp
# This means that the initial coordinates will be taken from the corresponding
# liquid simulation.
follow liq
$end

$compute
# name  method     property   protocols-and-corrections
dens    linear    density    liq
dhvap   linear    dhvap      liq    none    0.0
gamma   linear    gamma      slab
$end

$optimize
# maximum steps of MBAR sample optimization
maxsteps 0
# cutoff on number of samples used for MBAR optimization
ncut            0.15
# propname       ref       wei       tol   
dens          1378.8       2.0       1.0
dhvap           6.30       1.0       0.1  
gamma          11.75       1.0       0.2
$end