When you try to minimise, it will typically tell you the worst offending atoms in your system. Which you can then check visually using VMD etc and try and work out why it is an issue. Then you can adjust how the system was set up to fix the issue.
Also, if you just look at the system visually (though can be an issue with larger systems) if there is something that is really out of place, it can be easy to spot. Such as two molecules too close, interlocked, or severely distorted. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of Lum Nforbi Sent: Friday, 20 November 2009 9:19 AM To: [email protected] Subject: [gmx-users] How to check for bad contacts Hello, How do you check for bad contacts in a system that cannot be minimized? Thanks, Lum
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