[gmx-users] Martini Lipid Bilayer Simulation
jkrieger at mrc-lmb.cam.ac.uk
jkrieger at mrc-lmb.cam.ac.uk
Sat Sep 3 19:53:14 CEST 2016
Dear Prithvi,
This sounds like diffusion through the periodic boundaries to me and not a
problem at all. Try trjconv to fix it for visualisation as suggested at
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Best wishes
James
> Dear gmx users,
>
> I am trying to perform Martini CG simulations containing peptide helices
> embedded into POPC bilayer with Gromacs 5.1.2. I have prepared the system
> using the insane.py script provided on the Martini website. I am running
> the system using the mdp file (martini_v2.x_new.mdp) obtained from Martini
> website. The entries of the mdp file are as follows -
> ;
> ; 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 = 0.02
> nsteps = 200000000
> nstcomm = 100
> comm-grps = System
>
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 10000
> nstenergy = 1000
> nstxout-compressed = 10000
> compressed-x-precision = 100
> compressed-x-grps =
> energygrps = Protein POPC W
>
> ; 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 = cutoff
> coulomb-modifier = Potential-shift-verlet
> rcoulomb = 1.1
> epsilon_r = 15 ; 2.5 (with polarizable water)
> 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 = Protein POPC W
> tau_t = 1.0 1.0 1.0
> ref_t = 310 310 310
> Pcoupl = parrinello-rahman
> Pcoupltype = semiisotropic
> tau_p = 12.0 ;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
>
>
> As you may observe that I am running the simulation for 4 microseconds.
> The
> system runs perfectly fine till 4 microsecond. But at the end of 4
> microseconds I see that the POPC bilayer containing the peptide has moved
> till to the end (along Z-axis) of the simulation box. I also tried
> changing
> comm-grps = System to comm-grps = Protein POPC W. The bilayer still
> moved to the end of the box. Is it normal or is something not right?
>
> Thanking you,
>
> Prithvi Raj Pandey
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