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<DIV><FONT face=Arial size=2>Dear All,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>After ideally generated the Cl- location with the
"genion -random...", i started to run energy minimization by 200 steps "sd". I
noticed the Cl- move to the protein after few steps sd. One way to solve
this probem coming my mind is to fix Cl- during all the simulation (
including later production phase data collection).</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I tried to generate a new topology file, neu.top,
for the neutralized system. In addition to the "neu.top", four files
so named neu_A.itp, neu_B.itp, posre_A.itp, posre_B.itp were output
automatically, A for protein, and B is the Cl- respectively. </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>My question is how to specifically fix Cl-
only. I know one line in .mdp file: "define =-DPOSRES" is
generally for position restraint But could anyone please tell me how to
specifically fix either A or B, or both ( in my example)??? </FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Any of your suggestion is highly
appreciated!!!</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>nancy</FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=jdeng@adrik.bchs.uh.edu href="mailto:jdeng@adrik.bchs.uh.edu">Nancy
Deng</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 2:23
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [gmx-users] genion</DIV>
<DIV><BR></DIV>
<DIV><FONT face=Arial size=2>I have not get a chance to try yet. But I will
definitely keep you updated with my new result very soon.</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>
<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
<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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