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<blockquote type=cite class=cite cite>how can I manage to put a certain
number of water molecules in a box? I tried the genbox -nmol option with
-ci spc216.gro, but it didn't work out due to "more than one
residue". Can I convert the spc216.gro file so that it'll contain
only one residue (and how) or is there a better way? I need to have the
same number of molecules in a box, if I want to do free energy
calculations, right?</blockquote><br>
copy the spc216.gro to something like spc.gro or h2o.gro, then text edit
the file, deleting all put the first three atoms, adjust the second line
to the correct number of atoms, and reduce the box size. You can
then use genbox, but the code behind it isn't that good as you may end up
with some high energy overlaps. But with something as simple as water a
quick energy minimisation should sort that out.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Lecturer<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9574<br>
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