Dear all, I have a system composed of a trimeric protein and a double stranded DNA. I would like to calculate the distance between the center of mass (com) of the protein and the com of the DNA (I am working with the NVT equilibration trajectory as an example). I tried:
gmx distance -f nvt.trr -s nvt.tpr -select 'com of group Protein plus cog of group DNA' -xvg none -oall -rmpbc This gave distances that seem too long. Then I created a trajectory removing the PBC: gmx trjconv -f em.gro -s em.tpr -o whole.pdb -pbc nojump gmx trjconv -f nvt.trr -o whole.xtc -s whole.pdb -pbc nojump And calculated the distances again: gmx distance -f whole.xtc -s whole.pdb -select 'com of group Protein plus cog of group DNA' -xvg none -oall -rmpbc This gives reasonable results, different from the previous call to gmx distance. In an attempt to avoid calculating the whole.xtc trajectory I gave a pdb file that doesn't have broken molecules: gmx distance -f nvt.trr -s whole.pdb -select 'com of group Protein plus cog of group DNA' -xvg none -oall -rmpbc But this still gives the wrong result. I thought the flag -rmpbc would make molecules whole, but apparently it doesn't in my case. Is there a way to calculate the distance directly from the original trajectory? Thanks in advance, Ramon -- Ramon Crehuet Cientific Titular (Assistant Professor) Institute of Advanced Chemistry of Catalonia IQAC - CSIC scholar.google.es/citations?user=PIHmEiwAAAAJ orcid.org/0000-0002-6687-382X publons.com/a/1018637/ twitter.com/rcrehuet ramoncrehuet.wordpress.com Tel. +34 934006116 Jordi Girona 18-26 08034 Barcelona (Spain) -- 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.
