[gmx-users] angular com removal on DNA

[David van der Spoel]

Mu Yuguang (Dr) wrote:

>HI david,
>But it does not work
>
>It saids ( using gromacs3.3)
>ERROR: invalid enum 'Linear Angular' for variable comm-mode, using
>'Linear'
>  
>
I see, it wants the same algorithm for both. That's a limitation. Please 
test it.

>It works only I use one group
>comm-mode                = Angular 
>  
>
>>; group(s) for center of mass motion removal
>>comm-grps                = DNA
>>    
>>
>
>Here I worry about the SOL part, how can we treat that?
>
>Dr. Yuguang Mu
>Division of Structural and Computational Biology
>School of Biological Sciences
>Nanyang Technological University
>60 Nanyang Drive 
>Singapore 637551
>Tel: 63162885
>Fax: 67913856
> 
>
>-----Original Message-----
>From: gmx-users-bounces at gromacs.org
>[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
>Sent: Monday, December 05, 2005 4:06 PM
>To: Discussion list for GROMACS users
>Subject: Re: [gmx-users] angular com removal on DNA
>
>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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>>>   
>>>
>>>      
>>>
>>-
>> 
>>
>>    
>>
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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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