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!
Duan
>[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
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