[gmx-users] Exploding molecules

Frederic Leroy frederic.leroy at urv.net
Wed Aug 31 19:26:23 CEST 2005

Jeffrey Chua wrote:

> 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 electrostatics).
> thanks
> jeffchua
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I am simulating a sysytem similar to yours: An alcohol in water. I also 
use the OPLSAA potential for the alcohol. Everything is OK if I use an 
SPC/E model for the water. The problem comes when I try to use a TIP4P 
model. This makes me think about a problem with the constraints to be 
used to make the water being rigid.
If anybody has experience on this question... Many thanks by advance.

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