[gmx-users] water-air interface

[Mark Abraham]

On 1/12/2010 2:29 PM, 铁锋 彭 wrote:
> Hi everyone,
>
> I first created 3 x 3 x 3 nm water, 895 water using genbox. Then i used
>
> editconf -bt triclinic -f tension.gro  -o conf.gro  -c  -box  3 3 9  
> -angles 90 90 90
>
> make the water in x=y=3, z=9 nm box.
>
> Then
> grompp -f em.mdp -c conf.gro -p topol.top -o em.tpr -po mdout2.mdp 
> -maxwarn 10
>
> mdrun -v -s em -e pr -o pr -c after_pr
>
> Steepest Descents:
>    Tolerance (Fmax)   =  5.00000e+01
>    Number of steps    =       100000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -2.26219e+04 Fmax= 1.42837e+04, 
> atom= 379
> Step=    1, Dmax= 1.0e-02 nm, Epot= -2.54567e+04 Fmax= 5.60900e+03, 
> atom= 1870
> Step=    2, Dmax= 1.2e-02 nm, Epot= -2.83385e+04 Fmax= 2.94370e+03, 
> atom= 283
> Step=    3, Dmax= 1.4e-02 nm, Epot= -3.05598e+04 Fmax= 1.45800e+03, 
> atom= 2077
> Step=    4, Dmax= 1.7e-02 nm, Epot= -3.28940e+04 Fmax= 9.07848e+02, 
> atom= 1726
> Step=    5, Dmax= 2.1e-02 nm, Epot= -3.49312e+04 Fmax= 1.90443e+03, 
> atom= 1726
> Step=    6, Dmax= 2.5e-02 nm, Epot= -3.55885e+04 Fmax= 1.64255e+03, 
> atom= 1726
> Step=    7, Dmax= 3.0e-02 nm, Epot= -3.62927e+04 Fmax= 1.83479e+03, 
> atom= 1726
> Step=    8, Dmax= 3.6e-02 nm, Epot= -3.68613e+04 Fmax= 2.20746e+03, 
> atom= 1726
> Step=    9, Dmax= 4.3e-02 nm, Epot= -3.73153e+04 Fmax= 2.09106e+03, 
> atom= 1726
>
> t = 0.010 ps: Water molecule starting at atom 1726 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> Step=   10, Dmax= 5.2e-02 nm, Epot= -3.77143e+04 Fmax= 7.92103e+04, 
> atom= 1727
> Step=   26, Dmax= 1.9e-06 nm, Epot= -3.25046e+04 Fmax= 2.08556e+05, 
> atom= 1930
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 50
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 27 steps,
> but did not reach the requested Fmax < 50.
> Potential Energy  = -3.7714320e+04
> Maximum force     =  7.9210281e+04 on atom 1727
> Norm of force     =  2.0394656e+03
>
> grompp -f grompp.mdp -c after_pr.gro -p topol.top -o run.tpr -po 
> mdout3.mdp  -maxwarn 10
>
>
>
> uqtpeng1 at ce102-0419:~/water/surfacetension/339$ mdrun -v -s run -e pr2 
> -o pr2 -c after_pr2 -g prlog >& pr.job &
> Program mdrun, VERSION 4.0.7
> Source code file: ../../../../src/mdlib/nsgrid.c, line: 348
>
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
>
> So my problem is whether my EM result is good?
>

No, it isn't. There's at least one bad water molecule, like the output said.

>
> and why the Number of grid cells is zero??
>

Because the system imploded.

Mark
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