[gmx-users] The energy minimization....

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 16 18:03:27 CEST 2007

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...

>  >mjduan at smail.hust.edu.cn 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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