Merge branch 'main' of gitlab.com:hseara/spring_school2023_notebooks

; STANDARD MD INPUT OPTIONS FOR MARTINI 3.x

; Updated 30 Jan 2017 by PCTS

;

; for use with GROMACS 5

; TIMESTEP IN MARTINI 

; Default timestep of 20 fs. 

integrator               = sd

dt                       = 0.02

nsteps                   = 500000 ; 10 ns

nstcomm                  = 100

comm-grps		 = 

nstxout                  = 0

nstvout                  = 0

nstfout                  = 0

nstlog                   = 100000

nstenergy                = 5000

nstxout-compressed       = 50000

compressed-x-precision   = 100

compressed-x-grps        = 

; NEIGHBOURLIST and MARTINI 

; To achieve faster simulations in combination with the Verlet-neighborlist

; scheme, Martini can be simulated with a straight cutoff. In order to 

; do so, the cutoff distance is reduced 1.1 nm. 

; Neighborlist length should be optimized depending on your hardware setup:

; updating ever 20 steps should be fine for classic systems, while updating

; every 30-40 steps might be better for GPU based systems.

; The Verlet neighborlist scheme will automatically choose a proper neighborlist

; length, based on a energy drift tolerance.

;

; Coulomb interactions can alternatively be treated using a reaction-field,

; giving slightly better properties.

; Please realize that electrostVatic interactions in the Martini model are 

; not considered to be very accurate to begin with, especially as the 

; screening in the system is set to be uniform across the system with 

; a screening constant of 15. When using PME, please make sure your 

; system properties are still reasonable.

;

; With the polarizable water model, the relative electrostatic screening 

; (epsilon_r) should have a value of 2.5, representative of a low-dielectric

; apolar solvent. The polarizable water itself will perform the explicit screening

; in aqueous environment. In this case, the use of PME is more realistic.

cutoff-scheme            = Verlet

nstlist                  = 20

ns_type                  = grid

pbc                      = xyz

verlet-buffer-tolerance  = 0.005

coulombtype              = reaction-field 

rcoulomb                 = 1.1

epsilon_r                = 15	; 2.5 (with polarizable water)

epsilon_rf               = 0

vdw_type                 = cutoff  

vdw-modifier             = Potential-shift-verlet

rvdw                     = 1.1

; MARTINI and TEMPERATURE/PRESSURE

; normal temperature and pressure coupling schemes can be used. 

; It is recommended to couple individual groups in your system separately.

; Good temperature control can be achieved with the velocity rescale (V-rescale)

; thermostat using a coupling constant of the order of 1 ps. Even better 

; temperature control can be achieved by reducing the temperature coupling 

; constant to 0.1 ps, although with such tight coupling (approaching 

; the time step) one can no longer speak of a weak-coupling scheme.

; We therefore recommend a coupling time constant of at least 0.5 ps.

; The Berendsen thermostat is less suited since it does not give

; a well described thermodynamic ensemble.

; 

; Pressure can be controlled with the Parrinello-Rahman barostat, 

; with a coupling constant in the range 4-8 ps and typical compressibility 

; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration purposes, 

; the Berendsen barostat probably gives better results, as the Parrinello-

; Rahman is prone to oscillating behaviour. For bilayer systems the pressure 

; coupling should be done semiisotropic.

tcoupl                   = v-rescale 

tc-grps                  = SYSTEM

tau_t                    = 1.0   

ref_t                    = 310 

Pcoupl                   = berendsen 

Pcoupltype               = isotropic

tau_p                    = 4.0   ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422

compressibility          = 3e-4

ref_p                    = 1.0

gen_vel                  = no

gen_temp                 = 310

gen_seed                 = 473529

; MARTINI and CONSTRAINTS 

; for ring systems and stiff bonds constraints are defined

; which are best handled using Lincs. 

constraints              = none 

constraint_algorithm     = Lincs

free-energy 		 = yes

couple-lambda0 		 = none

couple-lambda1 		 = vdwq

couple-moltype 		 = TOLU

couple-intramol 	 = no

init-lambda-state 	 = 30

vdw_lambdas              = 1   1   1   1   1   1   1   1   1   1 1 0.95 0.9 0.85 0.8 0.75 0.7 0.65 0.6 0.55 0.5 0.45 0.4 0.35 0.3 0.25 0.2 0.15 0.1 0.05 0

coul_lambdas             = 1 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0    0   0    0   0    0   0    0   0    0   0    0   0    0   0    0   0    0   0    0 0

calc-lambda-neighbors 	 = -1

separate-dhdl-file 	 = no

sc_alpha 		 = 0.5

sc_sigma 		 = 0.3

sc_power 		 = 1

sc_coul 		 = no

awh 			 = yes

awh-potential 		 = umbrella

awh-nstout 		 = 50000

awh-nbias 		 = 1

awh-nstsample 		 = 100

awh-nsamples-update 	 = 10

awh1-error-init 	 = 10

awh1-equilibrate-histogram = no

awh1-target 		  = constant

awh1-growth 		  = exp-linear

awh1-ndim 		  = 1

awh1-dim1-coord-provider  = fep-lambda

awh1-dim1-coord-index 	  = 1

awh1-dim1-start 	  = 0

awh1-dim1-end 		  = 30

awh1-dim1-diffusion 	  = 0.001