I used -pbc nojump to remove pbc effect. trjconv 3.trr -s 3.tpr -pbc nojump -o 500-11.pdb
Basically I want to find the conformer close to center of box. Nilesh On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote: > On 18/10/2011 7:05 AM, Nilesh Dhumal wrote: > >> Hello, >> >> >> I have saved the coordinates of snapshot from trajectory in pdb file. >> >> >> The dimesnion of box in pdb file are >> 32.805 32.805 32.805 90.00 90.00 90.00 P 1 >> >> >> I am trying to find atoms close to center of box. >> >> >> there are atoms whose distance from center is more that ~17 A. My >> center coordinates are 0.0 0.0 0.0. >> >> How is it possible? >> > > Molecules diffuse across periodic boundaries during the simulation. > While computing interactions, mdrun corrects for periodicity on the fly, > but does not trouble itself to guess what manner of post-processing you > would like to do. There is a suggested trjconv workflow on the the GROMACS > website. I suggest you try it. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists