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

[Justin A. Lemkul]

He, Yang wrote:
> 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 ?
> 

Chapter 3 of the manual, the make_ndx man page, manual sections 8.1 and D.73 all 
provide relevant information.

Also:

http://wiki.gromacs.org/index.php/Index_File

-Justin

> 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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-- 
========================================

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

========================================