[gmx-users] The way how to restrict atoms in gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 17 01:58:35 CEST 2009

He, Yang wrote:
> Hi all users,
> I have used the position_restraints to restrict some atoms' activity but always it shows that Segmentation fault (core dumped).

It's 99% likely that this is not all that is going on - you have to read 
the end of the .log file and the standard output/error to diagnose what 
is going wrong. A segmentation fault is just a general expression that 
the software encountered an invalid memory reference - it can't help 
someone diagnose the cause. GROMACS almost always gives a real 
diagnostic message before doing so.

> I can not fix this problem after trying many methods and hence, I just wonder whether there are some other ways to restrict the atoms' movement in the gromacs.

There many sorts of restraints, there are freeze groups and there are 
constraints. Have a look in the manual.


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