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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