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

[Javier Cerezo]

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.

Javier

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
>
> 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?
>
> 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