Re: [gmx-users] PCA problems

Still no luck When I tried gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -pbc nojump I get a very strange trajectory and covar does not work with this I have also tried gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -fix transxy -pbc mol -s topol.tpr to generate a continuous

Re: [gmx-users] PCA problems

On Wed, 8 Jun 2016, Tsjerk Wassenaar wrote: Hey :) That usually gives a fitted ensemble that more closely retains the original RMSD values between all pairs of structures. This should read: ... a fitted ensemble of which the sum of the traces of all pairwise inner product matrices is

Re: [gmx-users] PCA problems

Hey :) > That usually gives a fitted ensemble that more closely retains the > original RMSD values between all pairs of structures. > This should read: ... a fitted ensemble of which the sum of the traces of all pairwise inner product matrices is closer to minimal. The pairwise RMSDs (and

Re: [gmx-users] PCA problems

Hi James, If your molecule shows some flexiblility, I would suggest using as a reference the structure of your original ensemble that produces the fitted ensemble with the lowest sum of RMSD values to that structure (or their square). That usually gives a fitted ensemble that more closely

Re: [gmx-users] PCA problems

ok thanks Tsjerk. I think that makes sense now. Best wishes James > Hi James, > > That's silly! Ambiguous means that the same structure can have multiple > solutions in a fit. The fit to a single reference structure (with more > than > three atoms) is never ambiguous. Can never, by definition! >

Re: [gmx-users] PCA problems

In addition to what Tsjerk said, may I point out that a publication by a colleague of mine treats exactly these problems that arise when trying to fit cartesian structures: http://scitation.aip.org/content/aip/journal/jcp/141/1/10.1063/1.4885338 Regards, Matthias On 06/08/2016 06:10 PM, Tsjerk

Re: [gmx-users] PCA problems

Hi James, That's silly! Ambiguous means that the same structure can have multiple solutions in a fit. The fit to a single reference structure (with more than three atoms) is never ambiguous. Can never, by definition! Now if you have two reference structures at hand, and they have (quite)

Re: [gmx-users] PCA problems

Thanks Tsjerk, Isn't the progressive fit supposed to rotate everything back into the same orientation without having to worry about inferring that orientation from a reference structure that doesn't align well? Each configuration should in theory align well to its predecessor all the way back to

Re: [gmx-users] PCA problems

Hi James, 'Spurious alignment' is the dependence of the resulting ensemble on the reference structure. Unfortunately, that's not solved by a progressive fit. Rather, in a progressive fit, the same configuration can have multiple orientations, based on the previous structures, which is also

Re: [gmx-users] PCA problems

Thanks very much for your help. I have tried with a .tpr file and there is an improvement but still breaks. Similarly when I apply the same protocol as I said previously, but with my peptide unbound I get the same problem however in this case the free peptide has no pbc conditions Best

Re: [gmx-users] PCA problems

Dear Teresa, That sounds like a periodic boundary issue to me. It could be fixed by using a tpr instead of a gro as the gmx covar manual says "All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account."

Re: [gmx-users] PCA problems

Hi Teresa, No, the peptide should not be broken. Did you remove jumps over PBC? The peptide will probably be severely distorted by filtering, though. Cheers, Tsjerk On Wed, Jun 8, 2016 at 8:49 AM, ingram wrote: > Dear GROMACS community > > I am trying to complete a