[gmx-users] Exploding molecules

Jeffrey Chua chuademon at gmail.com
Wed Aug 31 00:55:35 CEST 2005

dear friends,
 sorry, im resending this again...
 we are trying to do an md simulation of 1,2-cyclohexanediol (in water) 
using OPLSAA as forcefield but the runs always end up with a segmentation 
fault error. and when the trr files are converted and viewed using VMD, the 
molecule seems to have exploded, with the oxygens in the alcohol groups 
joining, and the whole molecule looks totally deformed. could it be because 
of electrostatics? can anyone suggest a way on how to go about this (without 
calculating for electrostatic potentials anymore if it is because of the 
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