Re: [gmx-users] least-squares fitting the second structure on the reference structure

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

Re: [gmx-users] least-squares fitting the second structure on the reference structure

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

Re: [gmx-users] least-squares fitting the second structure on the reference structure

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

[gmx-users] least-squares fitting the second structure on the reference structure

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