[gmx-users] g_rms alignment question

[Tsjerk Wassenaar]

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.

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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada