[gmx-users] g_rms alignment question

[Justin Lemkul]

On 12/4/12 3:10 AM, Tsjerk Wassenaar wrote:
> Hi Jia,
>
> You can use trjconv for custom fitting, and then feed the fitted trajectory
> to g_rms, not using fitting there. Either that's using -nofit or -fit none.
>

The same can be done in one step by using an index file with g_rms and choosing 
that group for fitting.

-Justin

> Cheers,
>
> Tsjerk
>
>
> On Tue, Dec 4, 2012 at 6:06 AM, Jia Xu <xujia.ruc at gmail.com> wrote:
>
>> Dear gromacs users,
>>      I have a trajectory of 500-atom system and would like to obtain RMSD of
>> all atoms but only aligned to residue 1-400 of a reference structure. Is
>> there any way to do this?
>>      Thank you so much!
>> Regards,
>> Jia
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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