[gmx-users] AFM pulling "group" question

Artit Wangperawong artitw at stanford.edu
Wed Feb 15 02:18:35 CET 2006

Do I have to use an index file for afm pulling?  If not, can I specify the
group as the atom or molecule being pulled?

Thanks, Art

Message: 1
> Date: Tue, 14 Feb 2006 22:29:12 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] AFM pulling "group" question
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <43F24BA8.6070902 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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.
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