[gmx-users] water genbox 3x3x0.8 EM not successful T not high

[Mark Abraham]

On 12/16/10, Javier Cerezo  <jcb1 at 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
> 
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