[gmx-users] Error in energy minimization

Justin Lemkul jalemkul at vt.edu
Tue Dec 18 01:20:13 CET 2012

On 12/17/12 7:17 PM, Kieu Thu Nguyen wrote:
> Dear All,
> When i do step EM, the output file .gro is separated into many step.pdb
> files .  And many errors "Water molecule starting at atom XXX can not be
> settled"  appears. And the potential energy is positive !
> What should i do to solve it ?

Please consult the list archive and Gromacs website first.  This is an error 
that is posted probably every other day.  Likely some of the thousands of posts 
in the archive will help, as well as 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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