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 <g...@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: crickzha...@gmail.com > To: gmx-users@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 > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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