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