Re: [gmx-users] RDF analysis with respect to center of mass of otein

I Justin, Thanks for your reply. Sadly, that’s not the only bizarre peak,as you can see on the next image: http://cl.ly/1B3B2y3I0o1R This is how it looks when i don’t consideren the COM as a reference: http://cl.ly/3m0d2W2y0N1Y What; i your opinion, could be the problem? I think i’ll just have to

Re: [gmx-users] RDF analysis with respect to center of mass of otein

On 9/19/14 4:54 PM, Carlos Navarro Retamal wrote: I Justin, Thanks for your reply. Sadly, that’s not the only bizarre peak,as you can see on the next image: http://cl.ly/1B3B2y3I0o1R This is how it looks when i don’t consideren the COM as a reference: http://cl.ly/3m0d2W2y0N1Y What; i your

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Not at all. I’m using the .xtc file that comes from the simulation. What do you mean with the nrexcl issue? Is there a way i can fix it? -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Hi Justin, Thanks again for all your help. If the problem is related to periodicity, why if i consider the whole protein i got ‘normal’ results? In any case i centered the protein with the following command: trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o

Re: [gmx-users] RDF analysis with respect to center of mass of otein

On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote: Hi Justin, Thanks again for all your help. If the problem is related to periodicity, why if i consider the whole protein i got ‘normal’ results? A normal (non-COM-based) RDF is an atom-based RDF, so periodicity doesn't affect the outcome.

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Carlos, You might want to try a PBC correction with -pbc nojump and another RDF calculation with the corrected trajectory. 2014-09-19 19:10 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 9/19/14 6:07 PM, Carlos Navarro Retamal wrote: Hi Justin, Thanks again for all your help. If the problem

Re: [gmx-users] RDF analysis with respect to center of mass of otein

Hi Marcelo, Thanks for your reply. Sadly it didn’t work either, so i’m trying to generate a new .tpr file by changing the nrexcl values just as Justin suggest. Hope this may works. Thanks the two of you. Best Regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied