Hi,<br>
<br>
Maybe as a note for any interested but unaware. In gromacs, the middle
of the box is always the middle of the *rectangular* box defined by the
first three numbers in the last line of the .gro file.<br><br>
Cheers,<br>
<br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 5/9/06, <b class="gmail_sendername">Anton Feenstra</b> <<a href="mailto:feenstra@few.vu.nl">feenstra@few.vu.nl</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;">
Diane Fournier wrote:<br><br>> Thank you !<br>><br>> I think the problem was indeed with building the box, because I redid<br>> the whole sequence on my drug-enzyme system (building the box with<br>> editconf, putting the water with genbox, and then writing my .tpr
<br>> file with grompp) and ran the same (test) position restraint md run,<br>> and this time, the ligand was inside. Will try minimisation again.<br><br>For the record: you have almost certainly had problems with PBC. mdrun
<br>will always place molecules 'in the box' (see manual). If your complex<br>happens to be on the box edge, one molecule may end up at a different<br>side of the box.<br><br>If, instead, your complex was in the middle of the box, as probably
<br>happend during your second setup sequence, pbc will not affect it, at<br>least not during EM when molecules tend not to move much.<br><br>Note, that for different box shapes, the 'middle of the box' may not be<br>what you expect.
<br><br><br>--<br>Groetjes,<br><br>Anton<br><br>* NOTE: New Affiliation, Phone & Fax numbers (below) *<br> _____________ _______________________________________________________<br>|
|
|<br>| _ _ ___,| K. Anton
Feenstra
|<br>| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |<br>|( | )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands |<br>| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
<br>|
| <a href="mailto:Feenstra@few.vu.nl">Feenstra@few.vu.nl</a> -
<a href="http://www.few.vu.nl/~feenstra/">www.few.vu.nl/~feenstra/</a>
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