<div>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?<br><br>Thanks, Art<br> </div><br><blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;" class="gmail_quote">
Message: 1<br>Date: Tue, 14 Feb 2006 22:29:12 +0100<br>From: David van der Spoel <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>Subject: Re: [gmx-users] AFM pulling "group" question
<br>To: Discussion list for GROMACS users <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:43F24BA8.6070902@xray.bmc.uu.se">
43F24BA8.6070902@xray.bmc.uu.se</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Artit Wangperawong wrote:<br>> Hi All,<br>><br>> My name is Art, and I am trying to run GROMACS with AFM pulling. I
<br>> noticed some entries on the GROMACS list and was wondering...How do<br>> you know what to input as your groups? In other words, where did some<br>> of you get "a_145-416" from?<br>> group_1 = a_145-416
<br>> group_2 = a_705-976<br>these are probably atom numbers. Based on the physics of your system you<br>have to decide which atoms to use in pulling. Any these names presumably<br>refer to groups in the index file.
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