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

Mark Abraham mark.abraham at anu.edu.au
Thu Aug 16 05:53:19 CEST 2007

> Hi, everyone:<br />I have meet some problem when simulating a protein and
> ATP complex. The energy minimization will stop after 14 steps. I had
> followed Mark's suggestion, did the protein and ATP eneryg minimization
> independently, and&#160; found that the protein can finish its
> minimization correctly, but&#160; the&#160; ATP 's minimization stopped
> after 14 steps. So it seems that there are something wrong with ATP. And
> Mark also said &quot;Probably your topology is broken&quot;, what is it
> means? What should I do now?

If you're going to quote somebody from here
http://www.gromacs.org/pipermail/gmx-users/2007-August/029115.html, don't
imply that they made the comment in relation to another post entirely
(unless you're trying to annoy them, that is).

I replied to the above question on the list yesterday here


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