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<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff size=2>Dr.
Dallas Warren,</FONT></SPAN></DIV>
<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff size=2>Yes, I
am trying to get the pure liquid benzene. I will try to do longer simulation and
see.</FONT></SPAN></DIV>
<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff size=2>I
tryied to run a EM with the 5*5*5 box, and use editconf to reduce the box
size, or in an other try with the density option but clusters
remain.</FONT></SPAN></DIV>
<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff size=2>Could
you tell me more about this program please, is it
downloadable?</FONT></SPAN></DIV>
<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff
size=2>thanks.</FONT></SPAN></DIV>
<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=421360004-25052004><FONT face=Arial color=#0000ff
size=2>Nicolas Dinter</FONT></SPAN></DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]<B>On
Behalf Of </B>Dallas Warren<BR><B>Sent:</B> mardi 25 mai 2004
12:37<BR><B>To:</B> Discussion list for GROMACS users<BR><B>Subject:</B> Re:
[gmx-users] Cluster pb<BR><BR></FONT></DIV>Nicolas,<BR><BR>
<BLOCKQUOTE class=cite cite="" type="cite">So I am quite surprised by my
results, could someone clarify my situation?<BR>How can I prevent cluster
from forming?</BLOCKQUOTE><BR>You are aiming to get pure liquid benzene,
right? In the second case, what was your density? By clustering,
it sounds like that you have some areas of the box with no molecules, i.e. it
is a vacuum. Running the simulation for longer with the pressure
coupling will eventually eliminate that.<BR><BR>In setting things up for
something like this, I distribute my molecules in a box that is about twice
the volume it is meant to be. Distribute them throughout the box, then
scale the box dimensions using editconf, then run the EM etc.<BR><BR>Also,
what are you using to distribute the molecules throughout the box? Not
sure how it is with the current versions, but I use to use genbox but it would
generate way too many clashes/overlaps between molecules and atoms to be of
much use at all. Now I use a program that someone here wrote that does a
far better job of random distribution.<BR><BR>Catch ya,<BR><X-SIGSEP>
<P></X-SIGSEP><B>Dr. Dallas Warren<BR></B><I>Research Fellow<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
9083<BR><FONT
face="Times New Roman, Times">--------------------------------------------------------------------------<BR><I>When
the only tool you own is a hammer, every problem begins to resemble a
nail.</FONT></I> </P></BLOCKQUOTE></BODY></HTML>