Hi Luciano,<br><br>Did you use -shuffle/-sort with grompp?<br>This can change the order of molecules. It will be changed in the .tpr and hence in all the structure output of mdrun (xtc/trr/gro).<br><br>Cheers,<br><br>Tsjerk
<br><br><div><span class="gmail_quote">On 11/1/07, <b class="gmail_sendername">Luciano Costa</b> <<a href="mailto:ltcnikit@gmail.com">ltcnikit@gmail.com</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;">
Hi gmx'users,<br><br>I runnning MD simulation that the *.gro output file was written to inverse, for instance:<br><br>The *.gro file was;<br><br>molecule<br>8<br>1MOL1 ...<br>1MOL1 ...<br>1MOL1 ...<br>1MOL1 ...<br>2MOL2 ...
<br>2MOL2 ...<br>2MOL2 ...<br>2MOL2 ...<br clear="all"><br>so after MD simulation the *.gro file was modified, for example:<br><br><br>
molecule<br>
8<br>
1MOL2 ...<br>
1MOL2 ...<br>
1MOL2 ...<br>
1MOL2 ...<br>
2MOL1 ...<br>
2MOL1 ...<br>
2MOL1 ...<br>
2MOL1 ...<br><br>Why do this occur in gro output file? would it will be that *.xtc and *.trr also was written as *.gro file? How can I to correct it? What do I do, please?<br><br>Thanks!<br><br>regards,<br><br>Luciano Tavares
<br><span class="sg"><br>-- <br>### Luciano Tavares da Costa ###<br> Laboratory of Molecular Spectroscopy<br>## IQ - University of Sao Paulo - Brazil ##<br> <a href="http://lem.iq.usp.br;ltcnikit@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://lem.iq.usp.br;ltcnikit@gmail.com
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>
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