[gmx-users] Check for bad contacts and/or reduce the timestep

[Justin A. Lemkul]

pragna lakshmi wrote:
> Hi,
>      I am trying to run protein-ligand complex simulation. At the final 
> MD run step it is showing the following error. Can anybody tell me the 
> solution for this error?
> 

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

There are hundreds of threads in the archive with the same issue and several 
possible solutions.  Please consult the link above (and referenced pages), as 
well as other posts.

If you need further help diagnosing the problem, please post a complete .mdp 
file, as well as a description of prior minimization and equilibration.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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