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 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. > > In any case i centered the protein with the following command: >> >> >> trjconv -f npt_production.xtc -s npt_production.tpr -center -pbc mol -o >>> traj_center.xtc >>> >>> >>> >>> >> and then i measure the RDF with the following one: >> >>> g_rdf -com -f traj_center.xtc -s npt_production.tpr -n index.ndx -o >>> TEST-carbons.xvg >>> >> >> But i’m still seeing these weirds peaks a short distance. >> > > Unlikely, but it could be related to nrexcl; that's what you should try > next. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Marcelo Depólo Polêto Biochemicist University of Viçosa - Brazil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.