[gmx-users] How to check for bad contacts

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Thu Nov 19 23:24:49 CET 2009

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
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Lum Nforbi
Sent: Friday, 20 November 2009 9:19 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] How to check for bad contacts



How do you check for bad contacts in a system that cannot be minimized?


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