Dear all,
I’m working on some simulations about the adsorption of protein on solid surfaces, which have slab geometry in the x-y plane. In order to reduce the amount of water molecules and at the same time to decrease the unphysical Coulomb interaction between periodic images in the z-direction, an empty layer should be added in the z-direction. To prevent the water molecules from evaporating into the vacuum layer, I’m going to use the wall option. However, there are some details that I’m not sure about.
What are your suggestions about the choice of wall_atomtype and wall_type? Is it necessary to leave some room for the two walls (or it may lead to high interaction energies between the walls and the system) and how to determine its height (in my simulations, I leave about 1.5 Å, respectively)? Does it have something to do with the wall_atomtype and wall_type?
When choose nwall=2, pressure coupling and Ewald summation can be used (it is usually best to use semi-isotropic pressure coupling with x/y compressibility set to 0). It means the wall can move in the z-direction? Can the pressure coupling be used in system with fixed atoms and how can we control/calculate the pressure of the mobile phase (as it has been discussed in the paper [Biointerphases 5, 85 (2010)] using the CHARMM package)?
When combing walls with the PME method, it is suggested the eward_geometry be set to 3dc and the wall_eward_zfac be 3. Does this mean there will be an empty layer whose height is 3 times the slab height added to increase the z-dimension of the box? And I’m not sure about the exact meaning of the “slab height”; it seems to be the length/width of the slab (as described in the paper [J. Chem. Phys. 111, 3155 (1999)]).
I’m so sorry for troubling you with so many questions. But I need your help badly and sincerely. Anyone can help me? Thank you!!
Bellow is an attachment of mdp file used in my simulation work. If there is anything wrong, please be kind to point it out. Thanks again!
Chunwang Peng
Room 302, Building 16，
Chemistry & Chemical Engineering，
South China University of Technology，
Tianhe District, Guangzhou
md.mdp
|
title = cyt-c on Au MD ; Run parameters integrator = md ; leap-frog integrator nsteps = 10000000 ; 2 * 10000000 = 20000 ps, 20 ns dt = 0.002 ; 2 fs comm-mode = Linear ; mode for center of mass motion removal
; Output control nstxout = 10000 ; save coordinates every 20 ps nstvout = 10000 ; save velocities every 20 ps nstenergy = 10000 ; save energies every 20 ps nstlog = 10000 ; update log file every 20 ps
; Selection of energy groups energygrps = Protein_HEM GLD ;Group(s) to write to energy file
; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints, GolP has been tested with lincs only constraints = hbonds ; bonds with H-atoms constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy
; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs rlist = 1.1 ; short-range neighborlist cutoff (in nm) ; Periodic boundary conditions pbc = xy ; 2-D PBC
; Method for doing Van der Waals vdw-type = switch rvdw-switch = 0.9 rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.1 ; short-range electrostatic cutoff (in nm) pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ewald_rtol = 1e-5 ewald_geometry = 3dc
; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes
; Temperature coupling is on tcoupl = Nose-Hoover ; Nose-Hoover thermostat tc-grps = Protein_HEM GLD Water_and_ions ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 300 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; nonuniform scaling of box vectors tau_p = 1.0 1.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, in bar compressibility = 0 4.5e-5 ; isothermal compressibility of water, bar^-1
; Velocity generation gen_vel = no ; Velocity generation is off
; Non-equilibrium MD stuff freezegrps = LOCK freezedim = Y Y Y
; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 2 wall_type = 9-3 wall_r_linpot = -1 -1 wall_atomtype = OWT3 OWT3 ; oxygen of TIP3P water in charmm27.ff wall_density = 33.4 33.4 wall_ewald_zfac = 3 |
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