[gmx-users] angular com removal on DNA

[Mu Yuguang (Dr)]

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?


-----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...

>
>  
>
>-----------------------------------------------------------------------
-
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.