Hi, David, Thank you for your help. I have fix it now. Have a nice weekend!
Dongsheng On Sat, 2006-06-24 at 21:53 +0200, David van der Spoel wrote: > Dongsheng Zhang wrote: > > Hello, everyone, > > > > I have a system with a nanotube and a polymer chain. First I did EM for > > the system in vacuum. After that, I added some water to my system, and > > tried to do EM again. This time I got some large force on some atoms. > > The messages are as folllows: > > Step= 0, Dmax= 5.0e-03 nm, Epot= -4.89150e+06 Fmax= 6.50095e+04, > > atom= 2463 > > Step= 1, Dmax= 5.0e-03 nm, Epot= -4.91505e+06 Fmax= 3.30822e+04, > > atom= 2463 > > Step= 2, Dmax= 6.0e-03 nm, Epot= -4.96938e+06 Fmax= 1.72511e+04, > > atom= 2463 > > Step= 3, Dmax= 7.2e-03 nm, Epot= -5.09757e+06 Fmax= 1.02066e+04, > > atom= 11109 > > Step= 4, Dmax= 8.6e-03 nm, Epot= -5.39186e+06 Fmax= 8.89407e+03, > > atom= 11109 > > Step= 5, Dmax= 1.0e-02 nm, Epot= -5.92594e+06 Fmax= 1.27715e+04, > > atom= 2464 > > Step= 6, Dmax= 1.2e-02 nm, Epot= -6.59458e+06 Fmax= 3.53621e+04, > > atom= 10534 > > Step= 7, Dmax= 1.5e-02 nm, Epot= -7.04583e+06 Fmax= 9.01766e+05, > > atom= 10534 > > Step= 8, Dmax= 1.8e-02 nm, Epot= -7.12198e+06 Fmax= 6.09737e+07, > > atom= 2464 > > Step= 14, Dmax= 6.7e-04 nm, Epot= -7.17427e+06 Fmax= 2.34996e+08, > > atom= 2463 > > Step= 16, Dmax= 4.0e-04 nm, Epot= -7.20472e+06 Fmax= 3.88459e+08, > > atom= 2464 > > Step= 18, Dmax= 2.4e-04 nm, Epot= -7.43615e+06 Fmax= 2.80954e+09, > > atom= 2463 > > Step= 21, Dmax= 7.3e-05 nm, Epot= -1.05082e+07 Fmax= 2.44979e+11, > > atom= 2464 > > Step= 25, Dmax= 1.1e-05 nm, Epot= -1.33633e+07 Fmax= 8.20246e+11, > > atom= 2463 > > Step= 27, Dmax= 6.5e-06 nm, Epot= -1.60347e+07 Fmax= 1.66408e+12, > > atom= 2463 > > Step= 29, Dmax= 3.9e-06 nm, Epot= -2.73531e+07 Fmax= 8.51628e+12, > > atom= 2463 > > Step= 32, Dmax= 1.2e-06 nm, Epot= -3.69604e+08 Fmax= 2.72010e+15, > > atom= 2463 > > Step= 33, Dmax= 1.4e-06 nm, Epot= -2.43314e+07 Fmax= 6.16803e+12, > > atom= 2463 > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > topology is wrong. check atom 2463 > > > > > I believe something is wrong here. Could anyone give me a hand how to > > fix it? Thank you very much! > > > > Have a nice weekend! > > > > Dongsheng > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
