[gmx-users] trjconv

[Apramita Chand]

Dear Justin,Gregory and Erik,
I'd asked earlier whether trjconv might change calculation of
properties.For diffusion probably, I could avoid applying trjconv before
analysis. For RDF, I checked before and after trjconv, there is a slight
difference in the RDFs. For instance , I'm studying a peptide-water-urea
system . On increasing concentration of urea, before I apply trjconv , the
interaction decreases . After applying trjconv , it increases slightly.
But how do I know for sure whether I should apply it or not?
Say I calculate properties like RDF,RMSD, etc after applying trjconv and
properties like diffusion,lifetimes without trjconv ; would that be right?
My peptide isn't broken or anything . It just seems to be partially out of
the box.

Please advise.


Regards,
Apramita