[gmx-users] trjconv behaving differently in 3.3.3 vs previous versions
nextgame at hotmail.com
Fri Mar 7 17:10:46 CET 2008
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: spoel at xray.bmc.uu.se
> To: gmx-users at 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.
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