[gmx-users] About using dodecahedron in editconf

[David van der Spoel]

qiwenpeng at sinap.ac.cn wrote:

>----- Original Message ----- 
>From: "David van der Spoel" <spoel at xray.bmc.uu.se>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Sent: Sunday, December 04, 2005 5:39 PM
>Subject: Re: [gmx-users] About using dodecahedron in editconf
>
>
>  
>
>>qiwenpeng at sinap.ac.cn wrote:
>>
>>    
>>
>>>Hello everyone!
>>>I use gromacs3.3/2.1 to simulate a DNA molecule. I want to use a box
>>>with a xy-hexagon to reduce the calculate time spenting.as follows:
>>>editconf -f 1.gro -o 2.gro -bt dodecahedron -box 2.5 2.5 10.5 -angles
>>>60 60 60
>>>But the result is:
>>>the program say:
>>>Volume: 22.8935 nm^3, corresponds to roughly 10300 electrons No
>>>velocities found
>>>system size : 2.139 2.286 4.242 (nm)
>>>diameter : 4.391 (nm)
>>>center : 0.000 0.000 -0.000 (nm)
>>>box vectors : 2.403 4.144 2.299 (nm)
>>>box angles : 90.00 90.00 90.00 (degrees)
>>>box volume : 22.89 (nm^3)
>>>shift : 1.875 1.875 0.884 (nm)
>>>new center : 1.875 1.875 0.884 (nm)
>>>new box vectors : 2.500 2.500 2.500 (nm)
>>>new box angles : 60.00 60.00 90.00 (degrees)
>>>new box volume : 11.05 (nm^3)
>>>It is obvious wrong!
>>>      
>>>
>>You can not have a dodecahedron with different box edges. You will have
>>to find the best triclinic box matching your requirements of
>>periodicity. Probably an elongated rectangle has the same effect.
>>
>>Do remember that in a box like you want the DNA should not be allowed to
>>rotate, you'll have to turn this off explicitly.
>>    
>>
>
>Sorry about that, How to turn off the rotate explicitly.
>  
>

Define two comm_groups, dna and rest and set comm_mode to angular

>Thank you very much!!
>  
>
>>>what can I do !!
>>>Thanks a lot
>>>
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>>>      
>>>
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