[gmx-users] Error in equilibration

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 26 06:32:49 CET 2008

s lal badshah wrote:
> Dear Justin,
> I try again by correcting the typo mistake I made, this time it gives 
> the following type of out put;

You still have a bad starting structure, even after your EM. Have a look 
at these atoms that are causing the actual error messages, since it 
might be a localised effect. Look for steric clashes, bonds that are too 
long, isolated water molecules, apparently non-formed bonds, etc.


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