Hi Abu,<br><br>Indeed. You have to add a parameter rototr = yes. Note that the changes in the .tpr file make it impossible to use these .tpr with other versions of gromacs and vice versa. Besides, you need a reference structure for the removal of the rotation/translation. This file has a fixed name: ref_conf.gro. The best thing to do is to take the .tpr file for the simulation and use editconf with an index file to generate ref_conf.gro from this .tpr (using the desired set of atoms).
<br><br>If you run into any trouble, please let me know. However, I'm rather busy at this moment, so trouble shooting may take a while.<br><br>Good luck,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 4/26/06, <b class="gmail_sendername">
Naser, Md Abu</b> <<a href="mailto:mn2@hw.ac.uk">mn2@hw.ac.uk</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="direction: ltr;">
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<div dir="ltr"><font color="#000000" face="Arial" size="2">Hi Tsjerk,</font></div><font color="#000000" face="Arial" size="2"></font></div>
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<div dir="ltr"><font color="#000000" face="Arial" size="2">Thanks for the link. I have been wondering how to select roto-translation option. Is it in the mdp file?</font></div>
<div dir="ltr"><font face="Arial" size="2"></font> </div>
<div dir="ltr"><font face="Arial" size="2">With regards,</font></div></div></div><div style="direction: ltr;"><span class="q">
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<div>Abu Naser
<div><pre></pre>
<div>School Of Life Sciences </div>
<div>Heriot-Watt University </div>
<div>Edinburgh EH14 4AS </div>
<div>Email: <a href="mailto:mn2@hw.ac.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">mn2@hw.ac.uk</a></div>
<div>Phone: +44(0)1314518265 </div>
<div>Fax : +44(0) 131 451 3009 </div>
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<font face="Tahoma" size="2"><b>From:</b> Tsjerk Wassenaar<br><b>Sent:</b> Wed 26/04/2006 12:05 PM</font></div><div style="direction: ltr;"><span class="e" id="q_10ad65a29d7eb39a_3"><font face="Tahoma" size="2"><br><b>To:
</b> Discussion list for GROMACS users<br><b>Subject:</b> Re: [gmx-users] comm-mode = Angular<br></font></span></div><div style="direction: ltr;"><br></div></div><div style="direction: ltr;"><span class="e" id="q_10ad65a29d7eb39a_5">
<div>Hi Abu,<br><br>In fact, I have it implemented in two versions (3.1.4 and 3.2.1), but haven't contributed it to the official code yet. At this point I don't have the time either :S However, you can download my versions at
<a href="http://md.chem.rug.nl/%7Etsjerk/GMX/" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://md.chem.rug.nl/~tsjerk/GMX/</a><br><br>Cheers,<br><br>Tsjerk<br><br>
<div><span class="gmail_quote">On 4/26/06, <b class="gmail_sendername">Naser, Md Abu</b> <<a href="mailto:mn2@hw.ac.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">mn2@hw.ac.uk</a>> wrote:
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<div dir="ltr"><font color="#000000" face="Arial" size="2">Hi Tsjerk,<br></font></div>
<div dir="ltr"><font color="#000000" face="Arial" size="2">I have been wondering whether Andrea Amadei and coworkers' method (</font></div>
<div dir="ltr"><font face="Arial" size="2">J. Chem. Phys. 112(1) pp. 9-23) has been implemented in Gromacs yet.</font></div>
<div dir="ltr"><font face="Arial" size="2"></font> </div>
<div dir="ltr"><font face="Arial" size="2">With regards,</font></div>
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<div dir="ltr"><font color="#000000" face="Arial" size="2"></font> </div></div>
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<div>Abu Naser
<div><pre></pre>
<div>School Of Life Sciences </div>
<div>Heriot-Watt University </div>
<div>Edinburgh EH14 4AS </div>
<div>Email: <a href="mailto:mn2@hw.ac.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">mn2@hw.ac.uk</a></div>
<div>Phone: +44(0)1314518265 </div>
<div>Fax : +44(0) 131 451 3009 </div>
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<font face="Tahoma" size="2"><b>From:</b> David van der Spoel<br><b>Sent:</b> Tue 25/04/2006 7:32 PM<br><b>To:</b> Discussion list for GROMACS users<br><b>Subject:</b> Re: [gmx-users] comm-mode = Angular<br></font><br></div>
<div><pre>Naser, Md Abu wrote:<br>> Hi All,<br>> <br>> Dose anyone know any literature regarding comm-mode = Angular option?<br>it just sets the overall angular momentum to zero.<br><br>> With regards,<br><br>
> Abu Naser<br>> <br>> School Of Life Sciences<br>> Heriot-Watt University<br>> Edinburgh EH14 4AS<br>> Email: <a href="mailto:mn2@hw.ac.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
<br>mn2@hw.ac.uk</a> <mailto:<a href="mailto:mn2@hw.ac.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">mn2@hw.ac.uk</a>><br>> Phone: +44(0)1314518265<br>> Fax : +44(0) 131 451 3009<br>
> <br><br>> <br>> <br>> <br>> <br>> <br>> ------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list
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</pre></div></div><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org
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http://www.gromacs.org/mailing_lists/users.php</a><br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen <br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br></div>
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</a><br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen
<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>