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
uqtpe...@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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