Dave, I am using it for visualization for now. -pbc mol gave me the same output as -pbc whole, which was a cubic box with broken protein. -pbc atom gave the dodecahedron box and intact protein. But since the functionality of -pbc mol has changed, and may not be applicable to visualization purposes, it is then not a bug. Judging from your reply, I seem to get the feeling that -pbc atom might not be a wise idea later on if I do actual analysis of the MD trajectory.
---------------------------------------- > Date: Fri, 7 Mar 2008 16:50:50 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous > versions > "did not work" is not good enough a description. However, the > functionality has changed, intentionally. The -pbc atom breaks molecules > and should be used with care (for visualization only). So hence I > presume this is not a bug. _________________________________________________________________ _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
