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

[rob yang]

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.

-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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