Hi Yuguang,<br>
<br>
To obtain a hexagonal prism, use editconf with option -angles 60 90 90
and vector lengths appropriate for your system. I assume you will use
it for an infinite DNA strand? Otherwise it may give trouble with
rotations, unless you use a rotational constraint algorithm.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 9/16/05, <b class="gmail_sendername">Mu Yuguang (Dr)</b> <<a href="mailto:YGMu@ntu.edu.sg">YGMu@ntu.edu.sg</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;">
Dear All,<br>Is there a way to use hexagonal prism condition (good for DNA fiber) in<br>gromacs ?<br><br>Dr. Yuguang Mu<br>Division of Structural and Computational Biology<br>School of Biological Sciences<br>Nanyang Technological University
<br>60 Nanyang Drive<br>Singapore 637551<br>Tel: 63162885<br>Fax: 67913856<br><br>-----Original Message-----<br>From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a><br>[mailto:<a href="mailto:gmx-users-bounces@gromacs.org">
gmx-users-bounces@gromacs.org</a>] On Behalf Of Mark Abraham<br>Sent: Friday, September 16, 2005 12:33 PM<br>To: Discussion list for GROMACS users<br>Subject: Re: [gmx-users] box type in gro file<br><br>> In gro file the last line gives the information of periodic box.
<br>Besides<br>> first three numbers of a,b,c, what other numbers mean?<br><br>See <a href="http://www.gromacs.org/documentation/reference_3.2/online/files.html">http://www.gromacs.org/documentation/reference_3.2/online/files.html
</a><br><br>They give the vectors describing the periodic box, which need not be<br>rectangular, of course.<br><br>Mark<br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
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gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen
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