[gmx-users] help: z-direction component of box vector becomes 0.00000 when using pdc = xy after

[Yinhe Zhang]

Hi, all

There are some things confusing and resulting in error when I run mdrun for
energy minization and md.

I use Gromacs 4.0.4 to simulate electroosmotic flow in slab geometry with
only 2 dimensional
periodic boundary (x and y), the system is aqueous solution with some ions,
eg. CL- and Na+,
flowing through a plate channel, with external electrical field applied
along x-direction, the height of channel
is z-direction.

Coulomb interactions are computed with PME, and use pbc=xy, after running
EM, all ouput tpr box sizes
in z-direction becomes zero, eg. originally the box size is
4.50000,4.50000,3.90000, after EM, it became
4.50000,4.50000,0.00000. so I can't use the output gro of EM for the MD run.

Did someone encounter this before and can give me some suggestion for my mdp
setup?

Thanks in advance.

(sorry for bad English expressions)

some options for mdp file of mine are here:

pbc                           = xy
rlist                           = 1.1
rcoulomb                   = 1.1
rvdw                          = 1.1

; electrostatics
coulombtype              = PME
fourierspacing             = 0.12
;fourier_nx                  =
;fourier_ny                  =
fourier_nz                    = 30
pme_order                   = 4
 dim
ewald_geometry          = 3dc           ; IMPORTANT
optimize_fft            = yes           ;

nwall                     = 2
wall_type               = 10-4
;wall_r_linpot          =
wall_atomtype        = SI  SI
wall_density           = 7.12 7.12
wall_ewald_zfac     = 3

; NEMD
acc_grps                        = WA  WAb  WAu
accelerate                      = 0.0 0.0 0.0  0.0 0.0 0.0  0.0 0.0 0.0
freezegrps                      = WA  WAb  WAu
freezedim                       = Y Y Y  Y Y Y  Y Y Y
; Electric fields
E_x                             = 1 -0.55 0


Regards,
Yinhe Zhang
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