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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=sabroggio@yahoo.com.br href="mailto:sabroggio@yahoo.com.br">Sabrina
Costa</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, January 19, 2005 11:29
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] nonbonded LJ
parameters</DIV>
<DIV><BR></DIV>
<DIV>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hy all,
<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I trying
to understand differences between two parametrization for the LJ parameters
for the Fluor atom looking for the equilibrium distance and the energy at this
point, using some atoms of interest in the system TFE-Water.
<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">I try to
reproduce the parameters in ffG43a1nb.itp using the geometrical approach
C12(i,j)=sqrt(C12(i,i)*C12(j,j). My surprise is that in the atom list we
have:<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">[
atomtypes ]<BR>;name
mass charge
ptype
c6
c12<BR> O
0.000 0.000 A
0.0022619536 7.4149321e-07<BR> OA
0.000 0.000 A
0.0022619536 1.505529e-06</SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> OW
0.000 0.000 A
0.0026173456 2.634129e-06<BR>
N 0.000
0.000 A 0.0024364096
1.692601e-06<BR> F
0.000 0.000 A
0.0011778624 7.6073284e-07<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">while
<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">[
nonbond_params ]<BR>; i j
func
c6
c12
c12=sqrt(c12(i)*c12(j)<BR>
OA O 1
0.0022619536
1.380375e-06
1.0565697e-06<BR>
OA OM 1 0.0022619536
2.258907e-06 <BR>
OW O 1
0.0024331696
1.825875e-06
1.3975653e-06<BR>
OW OM 1 0.0024331696
2.987943e-06
<BR> OW
OA 1 0.0024331696
1.991421e-06
1.991421e-06 - !!!!!!!!<BR>
N O 1 0.0023475616
2.185875e-06
1.1202911e-06<BR>
N OM 1 0.0023475616
3.577063e-06
<BR> N
OA 1 0.0023475616
2.384061e-06
1.596327e-06<BR>
N OW 1 0.0025252576
3.153489e-06
2.111523e-06<BR>
F O 1
0.0016322592
7.5105142e-07
7.5105142e-07 !!!!!!<BR>
F OM 1 0.0016322592
7.5105142e-07
<BR> F
OA 1 0.0016322592
1.505529e-06 1.0701894e-06<BR>
F OW 1 0.0017558112
1.991421e-06
1.4155806e-06
<BR>
F N 1 0.0016940352
2.384061e-06
1.1347322e-06<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">As you
can see some values follows the rule others no. The question is? Am I wrong
in use the rule to obtain the combinations for different atoms i and j ?
In this case how can I obtain these values ? By the other hand, if this is not
the case, what is wrong ?</SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hi
Sabrina</SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">The
Gromos van der walls parameters for an atom pair I,J are derived from the
relations stated by you.</SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">But, and
there's always a but, since gromos f.fs does not contain a special term in the
interaction function in order to mimic hydrogen bonding properties of polar
atoms, their C12 (polar atoms) van der waals has been increased. I'm quoting
part of gromos manual. </SPAN></P>
<P class=MsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">So, when
dealing with polar atoms, the C12 is higher than the one defined in
[pairtypes] field.</SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Regards</SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Nuno</SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><o:p></o:p></SPAN> </P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> </SPAN><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Waiting for your reply, thanks a
lot<o:p></o:p></SPAN></P>
<P class=MsoNormal><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"> </SPAN><SPAN
style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Sabrina. <o:p></o:p></SPAN></P>
<P class=MsoNormal> <o:p></o:p></P></DIV>
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