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

[Yinhe Zhang]

Hi, Berk

Thank you for your reply, finally I solved this by modifying the mdp
options.

'Cause I want to use PME in 2-dimensional periodic system to compute
electrostatic, I have to
set up the virtual walls with mdp option nwalls=2 in Gromacs. It succeeded
to set up the simualtion system.

Originally,  I constructed the walls of  monocrystal SI with diamond lattice
structure, but setting nwalls=0 and pbc=xy, so it happened that the
z-direction component of box size in the resulting gro file is 0.00000.

But, could I set nwalls=2, but with wall_density=0.0 to just with two
virtual walls without any
density, i.e. without wall atoms?? So that the additonal virtual walls the
mdrun added will not affect my system 'cause I already have two walls.
---------------------------------------------------------
nwalls                 =2
wall_type             = 10-4          ;
wall_atomtype    = SI  SI        ;
wall_density        = 7.12 7.12     ; nm^{-2}, number density, 200 atom in
5.3x5.3nm^2
---------------------------------------------

Regards,
Yinhe Zhang


On Wed, May 6, 2009 at 4:54 PM, Berk Hess <gmx3 at hotmail.com> wrote:

>  Hi,
>
> I tried to reproduce this, but I did not succeed.
> mdrun always seems to write the correct z size in all output files.
>
> Are you sure mdrun outputs a file (and which file, if so),
> or is it another Gromacs program that produced the file with 0 z size?
>
> You can simply manually correct the size in the file.
> But please report back which program produced which incorrect file.
>
> Berk
>
> ------------------------------
> Date: Wed, 6 May 2009 00:39:18 +0800
> From: crickzhang1 at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] help: z-direction component of box vector becomes
> 0.00000 when using pdc = xy after
>
>
> 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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