Mark:<br />Thank you for your reply!<br />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:<br /><br />Step=    0, Dmax= 1.0e-02 nm, Epot= -1.88000e+04 Fmax= 1.71469e+04, atom= 421<br />Step=   14, Dmax= 1.2e-06 nm, Epot=          nan Fmax= 1.59347e+04, atom= 4214<br />Stepsize too small, or no change in energy.<br />Converged to machine precision,<br />but not to the requested precision Fmax < 1<br /><br />it's really strange for "Epot = nan". I think maybe there are something wrong with it even it said "Converged to machine precision".<br />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!<br /><br />Duan<br /><br /><br /><br />>mjduan@smail.hust.edu.cn wrote:<br /><br />>To reply to a list email, just reply as you would to any other email.<br /><br /><br />>The .top succeeded in minimizing the solvated structure, so that's a<br />>good start. I think I can see that I was being too subtle for you<br />>earlier with my suggestion that you think about observables that would<br />>tell you whether your topology was working. Have you looked at the<br />>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<br />>post-minimization on their own, and there were no significant warnings<br />>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.<br /><br />>Mark<br />