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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Take a look at the “-center” flag of trjconv. Together with “-pbc” (and maybe also “-ur”) it should be possible to center your molecules of interest in the
middle of the simulation cell.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>Im Auftrag von </b>rama david<br>
<b>Gesendet:</b> Donnerstag, 29. März 2012 07:18<br>
<b>An:</b> Discussion list for GROMACS users<br>
<b>Betreff:</b> [gmx-users] About movie in GROMACS<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">HI Gromacs Friends,<br>
I complete one simulation for 4 different molecule placed apart <br>
in box of dimension 4 4 4 ..<br>
when I used the trajectory I saw the one molecule interact with each other but they are
<br>
getting broken because of box..(Some part protruding from other side).<br>
To see movie I used the command <br>
1. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc nojump -dt 10 <br>
The molecules moving apart without any interaction <br>
<br>
2. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc whole -dt 10<br>
The molecules are interacting in cell ..<br>
but because of periodic cell , near the cell boundary the molecule <br>
interaction get remove and molecules come in cell from other side..<br>
( I know it is because of periodic boundary condition ..one goes from right <br>
hand side come in cell through left hand side )<br>
<br>
To see the four molecule interacting each other near also cell boundary , what command
<br>
I have to use ???<o:p></o:p></p>
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