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GROMOS force field builds the LJ parameters by multiplication of the
square-rooted parameters per atom type (hence the SQRT(C6) and
SQRT(C12) labels). In the case of the repulsion term (C12), up to
three of such parameters are possible: SQRT(C12(1)) SQRT(C12(2))
SQRT(C12(3)), when combined with other atoms, depending on the
desired repulsion strength (e.g. the enhanced C12(3) repulsion is
used to keep charged groups separated). Which of the three is used
depends on the combination of atoms, and is specified in an
(asymmetric) matrix (see pages 14 and 15 in the pdf pages of 45a3
and 54a6 force fields from the GROMOS site, or in the ifp file the
last lines for each atom type containing "1", "2" and "3"). For the
case of OA, this matrix specifies that the second C12 term is to be
used when OA encountes another OA. So, according, to the ifp line
you showed:<br>
<br>
C12(OA-OA) = SQRT(C12(2))_OA * SQRT(C12(2))_OA = 1.227E-3 *
1.227E-3 = 1.50553E-6<br>
<br>
Which is the same for 45a3 and 54a6 force fields.<br>
<br>
Differences in the parameters will show up only in the cases where
the SQRT(C12(1)) term for OA is to be used (e.g C12(OA-CH2))<br>
<br>
Javier<br>
<br>
El 09/12/11 16:12, Samuli Ollila escribió:
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cite="mid:9CB0363621298A489A883A6ECFC4A47D11326489@UWMBX01.uw.lu.se"
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<div style="direction: ltr;font-family: Tahoma;color:
#000000;font-size: 10pt;">Dear all,<br>
<br>
I was comparing Gromos 45a3 and 53a6 force fields and I found
something which I cannot understand. The atom type OA is
described in ffG45a3nb.itp as:<br>
;name at.num mass charge ptype c6 c12<br>
OA 8 0.000 0.000 A 0.0022619536
1.505529e-06<br>
and in ffG53a6nb.itp:<br>
OA 8 0.000 0.000 A 0.0022619536
1.505529e-06<br>
which are same parameters.<br>
<br>
However, according to Gromos developers the atom type OA has
been changed between Gromos 45a3 and 53a6. The parameters given
by Gromos developers for 45a3 are<br>
# IAC TYPE SQRT(C6) SQRT(C12(1)) SQRT(C12(2))
SQRT(C12(3))<br>
3 OA 0.04756 1.1250E-3
1.227E-3 0.0<br>
and for 53a6<br>
3 OA 0.04756 1.100E-3
1.227E-3 0.0<br>
<br>
The actual numbers are different for parameters used in Gromacs
since the way to write parameters is different.<br>
<br>
My problem is that there is difference in OA type between 45a3
and 53a6 in parameters given by Gromos developers but not in the
files distributed in Gromacs package. Can someone explain this?<br>
<br>
BR,<br>
Samuli Ollila<br>
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<br>
<pre class="moz-signature" cols="72">--
Javier CEREZO BASTIDA
Ph.D. Student
Physical Chemistry
Universidad de Murcia
30100, Murcia (SPAIN)
T: (0034)868887434</pre>
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