[gmx-users] Error in energy minimization

[Justin Lemkul]

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 
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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