[gmx-users] trjconv

Erik Marklund erik.marklund at kemi.uu.se
Tue Nov 29 09:08:10 CET 2016

Dear Apramita,

Unfortunately, the short answer is that you need to think it through. What is being calculated, and how is the trajectory information affected by trjconv? If you for instance apply trjconv -fit rot+trans prior to RDF calculations, you might influence the results.

Kind regards,

> On 29 Nov 2016, at 07:36, Apramita Chand <apramita.chand at gmail.com> wrote:
> 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
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