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

[David van der Spoel]

rob yang wrote:
> Dave,
> -pbc mol did not work, however -pbc atom did. Also noted here: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/
> Thank you.
"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.


> 
> -Rob
> ----------------------------------------
>> Date: Fri, 7 Mar 2008 07:42:41 +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
>>
>> rob yang wrote:
>>> Hi list,
>>> I have a system solvated in dodecahedron box. To visualize it, I used:
>>> trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole
>>> Version 3.3.3 gave me a cubic box with broken molecules while the previous versions gave me the right visualization on the same system.gro
>>>
>> try -pbc mol.
>> otherwsie you are welcome to submit a bugzilla.
>>
>>> Does anybody have any similar experiences? Thanks.
>>>
>>> -Rob
>>> _________________________________________________________________
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>>
>> -- 
>> David.
>> ________________________________________________________________________
>> 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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> 
> _________________________________________________________________
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se