[gmx-users] Position Restraints

[#ZHAO LINA#]

Thanks for your answer again.

I will restrain the heavy atoms only first.

Best regards,

lina
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Wednesday, September 22, 2010 11:43 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Position Restraints

#ZHAO LINA# wrote:
> Thanks for your answer.
>
> How can I tell which ones I should restrain? all no-H atoms? in most general situations.

For the sake of clarity in the archive, it's probably best to avoid broad
generalizations.  People can easily stumble upon a post and take it way out of
context.  A "general situation" might encompass a lot.  I will reiterate that if
you want to recapitulate the behavior of pdb2gmx with respect to typical
biomolecules, you should choose all non-H atoms.

If you have some other specialized application, I can make no recommendation,
nor can anyone else, in the absence of a more thorough description.

-Justin

>
> lina
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Wednesday, September 22, 2010 11:15 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Position Restraints
>
> #ZHAO LINA# wrote:
>>  Hi,
>>
>> When I used the genrestr to get the posre.itp specially,
>> I found it set all atom to be applied to.
>> Is that okay? How could I figure out which ones should not be set to.
>>
>> A little naive questions, but I do do not know.
>
> The answer depends on your needs.  When running genrestr without an index file,
> you can choose from any of the default groups.  If you provide an index file,
> any group can be chosen.
>
> The default behavior of pdb2gmx is to generate a posre.itp file that restrains
> all heavy (non-H) atoms.  You can do the same with genrestr if you want, but
> again, the atoms you want to restrain depend on your goals.
>
> -Justin
>
>> Thanks with regards,
>>
>> lina
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
MILES-IGERT Trainee
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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