[gmx-users] angular com removal on DNA

[David van der Spoel]

Mu Yuguang (Dr) wrote:

>Dear David,
>As you suggested, one can use 
>
>comm-mode                = Angular  Linear
>; group(s) for center of mass motion removal
>comm-grps                = DNA  SOL
>
>to removeal overall rotation on DNA and translation on SOL specifically.
>Is it ight?
>  
>
In principle yes, but please test it carefully before running a lot of 
production.

>
>-----Original Message-----
>From: gmx-users-bounces at gromacs.org
>[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
>Sent: Sunday, December 04, 2005 6:24 PM
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] About using dodecahedron in editconf
>
>qiwenpeng at sinap.ac.cn wrote:
>
>  
>
>>Dear David:
>>
>>Thank you very much !
>>
>>But I want to know why use this parameter?
>>
>>Is there is something special in the DNA simulating?
>> 
>>
>>    
>>
>No, but think that you have an elongated molecule in an elongated box 
>and that the molecule rotates by 90 degrees...
>
>  
>
>> 
>>
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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://xray.bmc.uu.se/~spoel
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