[gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 7 17:45:00 CET 2008

rob yang wrote:
> 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. 
that is correct.

but -pbc mol -ur compact should give you a dodecahedron but with intact 
molecules. If you have an example where -pbc mol gives you a broken 
molecule that is a bug, unless the protein was broken from the 
beginning, which it shouldn't be. If this is indeed the case then please 
submit a bugzilla.

> ----------------------------------------
>> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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