silvester.thu wrote: > Thanks Mark. > I also have doubted that the system was not at the minium stationary > point before, because I searched the mailing-list archive and found the > description below:
> > The author of this description was describing another problem which was > different from my question. But this descripment is helpful for me. In > this description, the author minimized the energy of the system to reach > the level -- Fmax<1e-9 -- which I do not know how to get to. I have Depending what termination criterion was satisfied in your EM, you might do better by increasing the number of steps, or decreasing the emtol .mdp file parameter (see manual 7.3) > tried my best to EM, but I only got Fmax<3e-4. In the mdrun_d step, > there is no warning, while in the g_nmeig_d step, there is a warning that > > /One of the lowest 6 eigenvalues has a non-zero value. > This could mean that the reference structure was not > properly energy minimized./ > > So the system may be not at the minimum stationary point. How can I make > the system to reach this point? As I suggested last time, perturbing it in a sensible manner and observing the behaviour is a way to test your minimization. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
