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<DIV><FONT face=Arial size=2>I tried again with the -random option. Seems to me
the problem fixed. The newly added ion is pretty far from the protein
and it is near the face of the water box. Since I use "pbc" in my later
simulation, so it looks fine.</FONT></DIV>
<DIV><FONT face=Arial size=2></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>nancy</FONT></DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=dallas.warren@vcp.monash.edu.au
href="mailto:dallas.warren@vcp.monash.edu.au">Dallas Warren</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">Discussion list for GROMACS users</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Tuesday, March 01, 2005 1:50
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] genion</DIV>
<DIV><BR></DIV>
<BLOCKQUOTE class=cite cite="" type="cite">Probably genion placed solvent
inside the protein, and you used genion without the -random option. In that
case it places the ion where the potential is most favorable, which will
usually be inside the protein.</BLOCKQUOTE><BR>Has that been fixed? I
haven't tried to use the option for awhile now, as last time I did that was
broken and it simply placed all ions along one face of the box.<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
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>
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