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

[He, Yang]

HI Justin,

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.

Yang
________________________________________
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.

-Justin

> 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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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