[gmx-users] AFM pulling "group" question

David van der Spoel spoel at xray.bmc.uu.se
Tue Feb 14 22:29:12 CET 2006

Artit Wangperawong wrote:
> Hi All,
> My name is Art, and I am trying to run GROMACS with AFM pulling.  I 
> noticed some entries on the GROMACS list and was wondering...How do 
> you know what to input as your groups?  In other words, where did some 
> of you get "a_145-416" from?
> group_1                  = a_145-416
> group_2                  = a_705-976
these are probably atom numbers. Based on the physics of your system you 
have to decide which atoms to use in pulling. Any these names presumably 
refer to groups in the index file.

> Thanks for your help,
> Art
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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://folding.bmc.uu.se

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