David,<br>
<br>
Thanks a lot. That helps a whole lot. <br>
<br>
(For the list: The reason I needed to do this is that I was getting
waters stuck into my protein when solvating; it would take them forever
(well, a very long time) to escape, and I needed a way to make sure
this wouldn't happen.).<br>
<br>
David<br><br><div><span class="gmail_quote">On 1/9/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;">
David Mobley wrote:<br>> Dear all,<br>><br>> genbox has a -vdwd option which specifies "default vdwaals distance".<br>> The documentation isn't too clear about this; does it override what<br>> genbox usually uses? Or is it only used for molecules which have no vdW
<br>> parameters or some such?<br>Second.<br><br>><br>> For anyone who cares: I'm trying to keep water somewhat further away<br>> from the protein when solvating than is typical, and I'm trying to<br>> figure out whether using -vdwd is a way to do this, or whether I'll have
<br>> to make a script to delete all of the waters within my desired cutoff<br>> distance from the protein.<br>You want to copy the vdwradii.dat file to your working directory and<br>edit that.<br>><br>> Thanks,
<br>> David<br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________<br>> gmx-users mailing list<br>> <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________
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