Hi Sven,<br><br>Just to add a word on Dallas' reply. Use a larger box, such that you get just over the number of water molecules you need. Then delete the surplus. Pressure coupling will fix the vacuum.<br><br>Cheers,<br><br>
Tsjerk<br><br><div><span class="gmail_quote">On 11/2/05, <b class="gmail_sendername">Dallas B. Warren</b> <<a href="mailto:Dallas.Warren@vcp.monash.edu.au">Dallas.Warren@vcp.monash.edu.au</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;">
Sven,<br><br>> I'm trying to solvate 200 molecules of Glycine in water and I need a<br>> certaine concentration in the box. How can I determine the<br>> number of water<br>> molecules to be added to the glycine. when I run the genbox
<br>> command it gives<br>> me 1712 water molecule and I need them to be 2650 instead.<br><br>Couple of options, save a smaller number of waters in a gro file and<br>tell genbox to add the correct number of those (not sure if it has
<br>improved, but this script use to get some molecules overlapping and with<br>bad contacts, so take care). Or adjust the dimensions of the box using<br>editconf until you get the correct number of water molecules added when
<br>you solvate it.<br><br>Catch ya,<br><br>Dr. Dallas Warren<br>Lecturer<br>Department of Pharmaceutical Biology and Pharmacology<br>Victorian College of Pharmacy, Monash University<br>381 Royal Parade, Parkville VIC 3010
<br><a href="mailto:dallas.warren@vcp.monash.edu.au">dallas.warren@vcp.monash.edu.au</a><br>+61 3 9903 9073<br>---------------------------------<br>When the only tool you own is a hammer, every problem begins to resemble<br>
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<br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands
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