normal logP calculation using martini3

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3 months 2 weeks ago #9524 by yogi@martini
logP calculation using martini3 was created by yogi@martini
I tried calculating logP (water-octanol) partition coefficient for Ethanol using martini3 and martini2. I got value of -1.0 (martini3) and -0.6 (martini2), the experimental value is -0.3. Simulated temperature is 298 K. The itps are used from their respective martini_solvents.itp file. What could be the source of discrepancy? Since there is no thermodynamic integration tutorial for martini3, I have used standard_mdp file given for martini3 and free energy mdp options from martini2 tutorial.

the run2.mdp file used for first window.
; 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 = 2500000 ; 50 ns
nstcomm = 10
comm-grps =

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 2500 ; 1000
nstenergy = 2500 ; 1000
nstxout-compressed = 2500 ; 1000
compressed-x-precision = 100
compressed-x-grps =
;energygrps = Group1 Group2

; 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 = 298
Pcoupl = Parrinello-Rahman
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

; With Polarizable water:
; lincs_warnangle = 90


;
; Free energy parameters
free-energy = yes
sc-power = 1
sc-alpha = 0.5
sc-r-power = 6

; Which intermediate state do we start with? Doesn't really matter, it leaves soon
;
init-lambda-state = 0

; What are the values of lambda at the intermediate states?
;
vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0

; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states
;
calc-lambda-neighbors = -1

; the frequency the free energy information is calculated. This
; frequency (every 0.2 ps) is pretty good for small molecule solvation.
;
nstdhdl = 100 ; saving for 25000 points normally tutorial used 10 for 4 ns simulation which is 20000 data points

; not required, but useful if you are doing any temperature reweighting. Without
; temperature reweighting, you don't need the total energy -- differences are enough
dhdl-print-energy = yes

; We are doing free energies with the ethanol molecule alone
couple-moltype = ETO
; we are changing both the vdw and the charge. In the initial state, both are on
couple-lambda0 = vdw
; in the final state, both are off.
couple-lambda1 = none
; we are keeping the intramolecular interactions ON in all the interactions from state 0 to state 8
couple-intramol = no

Kindly help

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2 months 2 days ago #9553 by riccardo
Replied by riccardo on topic logP calculation using martini3
Not sure what the problem is here. Why should Martini 2 and Martini 3 give the same logP for ethanol? The interaction matrix has been been almost completely recalibrated, bead types representing ethanol are different, and hence it's expected that ethanol models will be somewhat different between the 2 force field versions. logP agreement w.r.t. experimental data is what one should look at and that seems fine looking at the numbers you reported here.

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