<br>
Hi Phuong,<br>
<br>
There is no box in your simulation system; All coordinates are
Cartesian coordinates. Read the manual better with regards to periodic
boundary conditions or check JCC 18:1930 (1997) (or alternatively JCC
25:1037 (2004)) by Henk Bekker. You could also search the archive for
previous posts concerning periodic boundary conditions.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 2/11/06, <b class="gmail_sendername">Nguyen Hoang Phuong</b> <<a href="mailto:phuong@theochem.uni-frankfurt.de">phuong@theochem.uni-frankfurt.de</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;">
<br>Dear All,<br><br>I have performed simulations using truncated octahedral box. Three unit<br>vectors of the truncated octahedral box (t1, t2, t3) are related to their<br>counterpart (e1, e2, e3) in Cartesian coordinate system by the
<br>relationship listed in page 13 of the gromacs's manual.<br><br>If I want to analyse the trajectory, e.g. calculating the scalar product<br>between two vectors, calculating the distance etc. then I have to convert<br>the atomic coordinates obtained directly from simulations to Cartesian
<br>coordinate system first?<br><br>I am not sure about this since in page 12 of gromacs's<br>manual it was written that "even when simulation was performed in triclinic box, gromacs always put<br>the particles in a brick shaped volume. It means that the coordinates in
<br>the output traj. (simulated with truncated octahedral box) are always in<br>Cartesian system? Gromacs automatically convert the (t1, t2, t3) system to<br>the Cartesian coordinate system (e1, e2, e3) when output trajectory?
<br><br>Thanks for any explaination.<br><br>Phuong<br><br><br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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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>