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 <[email protected]> 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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