Hi,
Each frame of the trajectory is fitted to the reference structure
independently of the others... but not if you're using gmx confrms, which
only acts on a single frame anyway...
Mark
On Thu, Jun 23, 2016 at 12:11 AM Qasim Pars wrote:
> Hi Tsjerk,
>
> Thanks, I know that. I was wondering ho
Hi Tsjerk,
Thanks, I know that. I was wondering how does a second structure (for
instance third frame) fit mathematically onto the reference structure? I
understand the least-square fitting for only one data set but I couldn't
understand the the least-square fitting for two data sets that fit on e
Hi Qasim,
If you fit a trajectory, with trjconv -fit rot+trans, then each frame is
fit onto the reference.
Hope it helps,
Tsjerk
On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars wrote:
> Dear users,
>
> From GROMACS online manual:
> gmx confrms computes the root mean square deviation (RMSD) of tw
Dear users,
>From GROMACS online manual:
gmx confrms computes the root mean square deviation (RMSD) of two structures
after least-squares fitting the second structure on the first one.
My question is how GROMACS does least-squares fitting the second structure
(each frame of trajectory) on the