----- Original Message ----- From: Suman Chakrabarty <su...@sscu.iisc.ernet.in> Date: Saturday, March 7, 2009 17:24 Subject: [gmx-users] pbc interference with g_dist To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Hi, > > after spending a long time with a seemingly wrong result with g_dist, > I discovered that g_dist actually uses pbc and nearest image > convention to calculate the distance. > > As a result, the end-to-end distance of my polymer chain is calculated > as 1.5 nm, while actually it should be 12.44 nm (box length = 13.9422 > nm). Since I am interested in the end-to-end distance of the single > polymer chain irrespective of the position of the two ends, I would > like to know what would be the best way to go about it. Use trjconv or editconf to change the size of the box, or use the -pbc no option of g_mindist. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
