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

Berk Hess gmx3 at hotmail.com
Wed May 6 10:54:48 CEST 2009


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.


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       
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            
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

Yinhe Zhang

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