[gmx-users] restrict two atoms in a group using freezegrps
yang.he at mavs.uta.edu
Sun Apr 19 00:10:00 CEST 2009
Thank you for your reply. I wonder what you mean by saying that I can specify a custom index group as your group
to be frozen. Can you give me a example about this ?
Thank you very much.
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Saturday, April 18, 2009 11:59 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] restrict two atoms in a group using freezegrps
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.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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