[gmx-users] AFM pulling "group" question

[Maik Goette]

You need a pull.ppa where the pulling-vector, -group, etc. is defined.
You also need to attach an index file with the groups included.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Artit Wangperawong wrote:
> 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
>     <mailto: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
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: < 43F24BA8.6070902 at xray.bmc.uu.se
>     <mailto: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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