Hi All, I just wanted to let you know how I resolved my problem, in case anyone else experiences a similar problem in the future.
My structure spanned all four quadrants around the origin (i.e. the 4 vertices of my structure were (-x, -y), (-x,y), (x,-y), & (x,y)). I think because it spanned all 4 quandrants, this caused the molecule to jump from corner to corner within the box. Once I translated my molecule such that its coordinates were entirely within the positive x,y quandrant, the molecule no longer jumped around in the box. Best regards, Darrell Koskinen >Date: Sun, 17 May 2009 20:08:06 +1000 >From: Mark Abraham <mark.abra...@anu.edu.au> >Subject: Re: [gmx-users] Molecule Jumps >To: Discussion list for GROMACS users <gmx-users@gromacs.org> >Message-ID: <4a0fe206.4000...@anu.edu.au> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >darre...@ece.ubc.ca wrote: >> Hi All, >> I have an array of molecules above a grapehene sheet in my simulation. >> However, when I look at my trajectory file (.trr) in VMD the array of >> molecules is split into 4 sections with each section located at what >> looks to be the corners of the simulation box. And the graphene sheet >> does not stay stationary as it should, but rather jumps from corner to >> corner. I tried to resolve this problem by running the following command: >> >> trjconv -f traj.trr -o trajout.trr -center -pbc nojump >> >> However, this did not resolve the problem. Is there something else I need >> to do to resolve this problem? > >No, some combination of options to trjconv should work. Sometimes two >two separate invocations with separate options are needed. > >BTW "...does not stay stationary as it should" is not true... you're >wanting a certain feature for your visualization convenience, and during >the simulation GROMACS hadn't permitted you to choose which of the >infinite equivalent possibilities it should present in the trajectory. >You're choosing that now, *after* the fact. > >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
