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<DIV><FONT face=Tahoma><FONT face=Calibri>Thanks for your answer. I changed
the non-bond parameters in ffgmxnb.itp. like</FONT></FONT></DIV>
<DIV><FONT face=Tahoma><FONT face=Calibri>; i j
func a
b c6</FONT></FONT></DIV>
<DIV><FONT face=Tahoma><FONT face=Calibri>Zn
O 2
... ..... ....</FONT> </FONT></DIV>
<DIV><FONT face=Tahoma><FONT face=Calibri>But error occured..</FONT></DIV>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN><FONT
size=2 face=Tahoma> </FONT></P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN>ERROR 1
[file ffgmxnb.itp, line 270]:</P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN><SPAN
style="mso-spacerun: yes"> </SPAN>Trying to add Buck.ham (SR) while the
default nonbond type is LJ (SR)</P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt"
lang=zh-CN> </P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt"
lang=zh-CN> </P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN>ERROR 2
[file ffgmxnb.itp, line 271]:</P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN><SPAN
style="mso-spacerun: yes"> </SPAN>Trying to add Buck.ham (SR) while the
default nonbond type is LJ (SR)</P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt"
lang=zh-CN> </P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt"
lang=zh-CN> </P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN>ERROR 3
[file ffgmxnb.itp, line 272]:</P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN><SPAN
style="mso-spacerun: yes"> </SPAN>Trying to add Buck.ham (SR) while the
default nonbond type is LJ (SR)</P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt"
lang=zh-CN> </P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN><FONT
size=2 face=Tahoma>I think I have indicated that the function type is 2 (means
Buckingham). Anything else need to do with this ?</FONT></P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN><FONT
size=2 face=Tahoma>Also, I want to fix some atoms in the boundary and specify
displacement to some atoms, anayone knows how to do this? </FONT></P>
<P style="MARGIN: 0in; FONT-FAMILY: Calibri; FONT-SIZE: 11pt" lang=zh-CN><FONT
size=2 face=Tahoma>Thank you in advance.</FONT></P></FONT>
<BLOCKQUOTE
style="BORDER-LEFT: #000000 2px solid; PADDING-LEFT: 5px; PADDING-RIGHT: 0px; MARGIN-LEFT: 5px; MARGIN-RIGHT: 0px">
<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="FONT: 10pt arial; BACKGROUND: #e4e4e4; font-color: black"><B>From:</B>
<A title=gmx3@hotmail.com href="mailto:gmx3@hotmail.com">Berk Hess</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> Wednesday, February 18, 2009 11:39
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> RE: [gmx-users] combination
rules -- the part about the combinationrules</DIV>
<DIV><BR></DIV>Hi,<BR><BR>No pairtypes are for bonded pair
interactions,<BR>not for combinations of non-bonded interactions.<BR><BR>The
manual tells you how to do this:<BR>[ nonbond_params ]<BR>A_ii A_jj
2 a b c6<BR><BR>Berk<BR><BR>> Date: Wed, 18 Feb 2009
13:31:43 -0500<BR>> From: <A
href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</A><BR>> To:
<A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>>
Subject: [gmx-users] combination rules -- the part about the combination
rules<BR>> <BR>> For LJ interactions, use [ pairtypes ]. For Coulombics
there is <BR>> unfortunately no analogous solution. I am not clear about
exactly what <BR>> you want to do. What "parameters" are you interested in,
or by this do <BR>> you just mean LJ and Q?<BR>> <BR>> Chris.<BR>>
<BR>> -- original message --<BR>> <BR>> Hello,<BR>> I was
wondering how to set up parameters for interactions between <BR>> two
different atoms A and B. Since for Gromacs parameters are defined <BR>> to
each kind of atom, I cannot specify parameters between A and B. For <BR>>
Buckingham potential, the rule was:<BR>> A_ij=(A_ii * A_jj)^(1/2)<BR>>
So anyone know how to specify this value while not using the <BR>>
combination rules?<BR>> --snip--<BR>> <BR>> <BR>>
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