[gmx-users] Re:

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 15 17:04:55 CEST 2007

mjduan at smail.hust.edu.cn wrote:
> Dear Mark:

Please keep correspondence on the list for others to see and use.

> Thanks for your help about my problem of running GROMACS energy minimization. 
> I do what you suggestion,  and the protein's minization seems to be correct, it run
> about 300 steps and the Ep convergent finally, but the ATP's minimization stopped 
> at 14 stpes. So it means the ATP's topology is broken? what is it means? What should 
> I do?

So how do you think you would be able to tell whether either or both of
these chemical structures were in a sensible energy minimum? What
observables will be useful to you here?


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