[gmx-users] About using dodecahedron in editconf

[qiwenpeng at sinap.ac.cn]

----- 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.

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