MoJie Duan wrote: > Mark: > Thank you for your reply! > I have checked my topology file of the ATP, I think there isn't any > problem with it. When I do the grompp (only use the ATP molecule), there > is not any warning and error, it stopped at 14th step, and return the > following messege: > > Step= 0, Dmax= 1.0e-02 nm, Epot= -1.88000e+04 Fmax= 1.71469e+04, > atom= 421 > Step= 14, Dmax= 1.2e-06 nm, Epot= nan Fmax= 1.59347e+04, > atom= 4214 > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1 > > it's really strange for "Epot = nan". I think maybe there are something > wrong with it even it said "Converged to machine precision". > But when I do the full MD Simulation (not energy minimization), the > program said "Fatal error:Number of grid cells is zero. Probably the > system and box collapse d"!!! (there also isnot any warning and error in > grompp). I think the problem maybe caused by the energy minimization > step, but I really don't know why!
So look at your structures like I said last time! I'm not here to give my valuable time giving free advice in order to have it ignored... > >[EMAIL PROTECTED] wrote: > > >To reply to a list email, just reply as you would to any other email. > > > >The .top succeeded in minimizing the solvated structure, so that's a > >good start. I think I can see that I was being too subtle for you > >earlier with my suggestion that you think about observables that would > >tell you whether your topology was working. Have you looked at the > >before- and after-minimization structures to see whether they make > >sense according to your training at recognizing chemical structures > >that will be energy minima? If all of your components look reasonable > >post-minimization on their own, and there were no significant warnings > >or errors from grompp then your topolog ies probably are OK too. Then > >you should go back and approach your original problem of getting a > >working topology for your combination system. > > >Mark > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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