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<DIV><FONT face=Arial size=2>I made a mistake in the numbers, but the question
remains:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I ran the following command in
gromacs:</FONT></DIV>
<DIV><FONT face=Arial size=2>editconf -bt dodecahedron -f p61_vac_gro.gro -o
p61_vac_dod.gro -d 0.8</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>The equivalent command in amber:</FONT></DIV>
<DIV><FONT face=Arial size=2>solvateoct p61_vac.pdb TIP3PBOX 8.0</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>As far as I understand this, both command created a
box were the edges are 0.8 nm away from the solute. But the resulting image
distance (d in the manual) in gromacs is:</FONT></DIV>
<DIV><FONT face=Arial size=2>121.3092</FONT></DIV>
<DIV><FONT face=Arial size=2>and in amber:</FONT></DIV>
<DIV><FONT face=Arial size=2>110.5103716</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>This is makes a hugde difference in the number
of water atoms to add.</FONT></DIV>
<DIV><FONT face=Arial size=2>Does anyone has an explanation for this
paradox?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>kind regards,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>servaas</FONT></DIV></DIV></BODY></HTML>