On 12/16/10, Javier Cerezo <j...@um.es> wrote: > Could you please attach your minimization parameters (mdp file) and > grompp/mdrun commands? > > Your simulation box seems a bit strange for me. If you're using periodic > boundary conditions you have not a thin film, but an infinite bulk water > (remember pbc replicate the box in all directions). With such a small Z axis > you might have probles with the cut-off radius being longer than a particle > image. >
GROMACS enforces the minimum-image convention, so we can deduce that that rcoulomb was unreasonably short. > El 16/12/10 10:38, gromacs escribió: > > > >Hi, > > > >I want to simulate 3x3x0.8 water film (bulk water) first creat the water, > > > >genbox -cs -o film.gro -box 3 3 0.8 > > > >then, i EM the bulk water; > > > >Using steep, but > > > >t = 0.011 ps: Water molecule starting at atom 298 can not be settled. > >Check for bad contacts and/or reduce the timestep. > >Wrote pdb files with previous and current coordinates > Here's the first hint something is wrong. Don't ignore it and plow on! > > > > >then i run, and i get the result. I use NPT, and T=300K. I run several > >times, but the final T was still 411K. > > > >So what could i do to get EM process successful? > > > >And what is the reason ? why i can not control the T 300K? > Over what timescale did you equilibrate? Over what *separate* timescale did you observe? Mark > > > > >Energy Average RMSD Fluct. Drift Tot-Drift > >------------------------------------------------------------------------------- > >Potential -9496.38 136.145 135.455 -0.158085 -47.4256 > >Kinetic En. 2358.2 73.5876 73.5471 -0.0281891 -8.45676 > >Total Energy -7138.19 136.284 135.326 -0.186274 -55.8824 > >Temperature 411.945 12.8548 12.8477 -0.00492426 -1.47728 > >Pressure (bar) -1.66406 704.355 704.355 -0.00424907 -1.27473 > >Box-X 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 > >Box-Y 2.91791 0.0128965 0.0128789 -7.7826e-06 -0.00233479 > >Box-Z 0.778108 0.00343907 0.00343437 -2.07536e-06 -0.000622609 > >Density (SI)&nbs p; 1038.7 13.6165 13.5998 0.00778513 2.33555 > >Heat Capacity Cv: 12.49 J/mol K (factor = 0.000973754) > > > > > > > > -- > Javier CEREZO BASTIDA > Estudiante de Doctorado > --------------------- > Dpto. Química-Física > Universidad de Murcia > 30100 MURCIA (España) > Tlf.(+34)868887434 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > >
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