normal Density of martini water

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2 years 5 months ago - 2 years 5 months ago #8391 by yogi@martini
Density of martini water was created by yogi@martini
Hello experts,

I did a bulk water simulation. For which I took box of 1000 water beads, energy minimized it and did NPT simulation. For energy minimization and NPT simulation standard mdp file given at the site is used. The paper "Coarse Grained Model for Semiquantitative Lipid Simulations" gives water density of 0.99 g/cm^3 at 300 K. However, I am getting higher value. Here is the plot - https://imgur.com/hRzT92K

The simulation is done for 15 nanoseconds

The minimization and NPT mdp files are as follows:
MINIMIZATION.MDP
integrator = steep
nsteps = 1000
nstxout = 0
nstfout = 0
nstlog = 100

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

NPT MDP
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.

title = Martini

; TIMESTEP IN MARTINI
; Most simulations are numerically stable with dt=40 fs,
; however better energy conservation is achieved using a
; 20-30 fs timestep.
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.

integrator = md
dt = 0.03
nsteps = 500000
nstcomm = 100
comm-grps =

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxout-compressed = 1000
compressed-x-precision = 100
compressed-x-grps =
energygrps = system

; 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 = parrinello-rahman
Pcoupltype = isotropic
tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

gen_vel = no
gen_temp = 320
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

Please help.
Last edit: 2 years 5 months ago by yogi@martini.

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2 years 5 months ago #8392 by riccardo
Replied by riccardo on topic Density of martini water
The discrepancy is roughly 1%, and it can be explained by the change in mdp parameters. Your value is in great agreement with the value reported in Table 2 of  www.sciencedirect.com/science/article/pii/S0010465515003628  (see the "new" set of mdp parameters versus the "published" one).

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2 years 5 months ago #8393 by yogi@martini
Replied by yogi@martini on topic Density of martini water
Thank you Riccardo.

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