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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=ruben@akilonia.cib.csic.es
href="mailto:ruben@akilonia.cib.csic.es">Ruben Martinez Buey</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Wednesday, April 28, 2004 1:47
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] energy minimization
and ions</DIV>
<DIV><BR></DIV> <BR>Hi all,
<P>I want to energy minimize a structure (two proteins + 4 ligands) in a water
box (dodecahedron). The total charge is not 0. what should I do better: <BR>-
add the ions I need to avoid this charge. <BR>- add negative ions to
compensate the positive charges (Asn, Gln in the protein and positive charges
in the ligands) and positive ions to compensate negative charges (Glu, Asp in
the protein and ligands), so the total charge will be 0.
<P>
<P><FONT face=Arial size=2>Just neutralize the system. The two options that
you posed seem to me are the same, arent't they?</FONT>
<P><FONT face=Arial size=2>Regrads,</FONT>
<P><FONT face=Arial size=2>Nuno</FONT>
<P><FONT face=Arial size=2></FONT>
<P>Thanks in advance, <BR>Cheers, <PRE>Ruben</PRE> </BLOCKQUOTE></BODY></HTML>