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<DIV><FONT face=Arial size=2>I had no luck so far in equibrating a CHCL3
box.</FONT></DIV>
<DIV><FONT face=Arial size=2>I tried two things.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>1) I first started with a CHCL3 solvent box
(borrowed from AMBER).</FONT></DIV>
<DIV><FONT face=Arial size=2>Minimiz is ok and NVT run appears ok. However, when
I tried to switch to NPT,</FONT></DIV>
<DIV><FONT face=Arial size=2>I get the usual "pressure scaling more than 1%"
error. As I understand, this is a sign that</FONT></DIV>
<DIV><FONT face=Arial size=2>the box is not equilibrated. </FONT><FONT
face=Arial size=2>I increased pressure coupling (up to 2.5), but it did not
help.</FONT></DIV><FONT face=Arial size=2>
<DIV><BR>What can I do next?</DIV>
<DIV>Note that, at the end of the NVT (up to 1 ns, 300K, Berendsen),
"holes" appear in the box, while other regions</DIV>
<DIV>have higher density. I increased the cutoffs to 1.7(thinking
they are trying to evaporate) but it did not help. What am I doing
wrong?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>2) I tried to build the box myself using the genbox
command, but apparently genbox does not recognize</FONT></DIV>
<DIV><FONT face=Arial size=2>VdW radia for CHCL3 and genbox generate molecules
on top of each other.</FONT></DIV>
<DIV><FONT face=Arial size=2>The command is : genbox -ci chcl3.gro -nmol #
(where nmol is set to approximate the density of CHCL3).</FONT></DIV>
<DIV><FONT face=Arial size=2>What should I do? Should I add the CHCL3 atom types
to the vdwradii.dat file?</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Thanks</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Germana Paterlini</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
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