[gmx-users] question about walls for a simple water box

ramon reigada at ub.edu
Tue Oct 28 13:48:43 CET 2014


Dear Gromacs users,

Unfortunately I am failing with the use of the wall options using martini force field simulations.
However, I still want to make the last attempt to work with walls. The example is simple, I built a water box with 1000 water molecules, I minimized possible contacts (steep) and then I run a constant isotropic pressure (1bar) equilibration. I checked that he water density is the correct one (about 1000 gr/l) and then I tred to simulate the water box with pbc = xy, No pressure and walls in z=0 and z=zbox.
I set the wall_atomtypes to an alkane carbon bead (C1 in the martini force field) and try 9-3, 10-4 and 12-6 potentials with different values of wall_rlin (1, 10, 10…).
I use ewald summations for the electrostatic interactions and I set ewald_geometry =3dc and wall_ewald_zfac=3. See the mdp below.
In all the attemps, the water box broke in two pieces and water escapes to large positive or negative z values outside the initial water box.

could anyone tell me what is the problme with this simple simulation?

   thanks,

  Ramon

; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.0200
nsteps                   = 200000
; number of steps for center of mass motion removal =
nstcomm                  = 1


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 2000
nstvout                  = 2000
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 2000
nstenergy                = 2000
; Output frequency and precision for xtc file =
nstxtcout                = 2000
xtc_precision            = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 =
; Selection of energy groups =
energygrps               = W

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 10
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xy
nwall = 2
wall_atomtype = C1 C1
wall_type = 9-3
wall_density = 110 110
wall_r_linpot = 1 1
wall_ewald_zfac = 3
; nblist cut-off         =
rlist                    = 1.4
domain-decomposition     = no

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 15
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 10
fourier_ny               = 10
fourier_nz               = 10
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no
ewald_geometry = 3dc

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = Berendsen
; Groups to couple separately =
tc-grps                  = W
; Time constant (ps) and reference temperature (K) =
tau_t                    = 1.0
ref_t                    = 310
; Pressure coupling      =
Pcoupl                   = No



Aquest correu electrònic i els annexos poden contenir informació confidencial o protegida legalment i està adreçat exclusivament a la persona o entitat destinatària. Si no sou el destinatari final o la persona encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu rebut aquest correu electrònic per error, us preguem que n’informeu al remitent i que elimineu del sistema el missatge i el material annex que pugui contenir. Gràcies per la vostra col·laboració.

Este correo electrónico y sus anexos pueden contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no es el destinatario final o la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha recibido este mensaje electrónico por error, le rogamos que informe al remitente y elimine del sistema el mensaje y el material anexo que pueda contener. Gracias por su colaboración.

This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration.


More information about the gromacs.org_gmx-users mailing list