[gmx-users] angular com removal on DNA

[Mu Yuguang (Dr)]

HI david,
But it does not work

It saids ( using gromacs3.3)
ERROR: invalid enum 'Linear Angular' for variable comm-mode, using
'Linear'

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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