[gmx-users] restrict two atoms in a group using freezegrps

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 18 20:59:59 CEST 2009

He, Yang wrote:
> HI all users,
> I have tried  a simple case with two atoms using [position_restraints] but always it shows the same error :
> Segmentation fault (core dumped)
> But after I don't use the position_restraints for one atom and then I can run the case smoothly. It seems that the gromacs doesn't recognize this [position_restraints];

That may just indicate instability due to the restraints themselves; i.e., 
fixing atomic positions leads to a crash.

> Then, I tried the freezegrps but it seems to restrict a whole group. Here, I wonder whether I can just use this method to restrict several atoms in a whole group and how to do that.

Like any other Gromacs tool, you can specify a custom index group as your group 
to be frozen.


> Thank you for your any suggestions.
> Yang
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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