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The reason is simple: they shall be different. You may notice that
gen_pair is "no" in ffG43a.itp. No generation of LJ parameters with the
combination rule will be used for this force field. During the design
of force fields, some opt for automatic generation from the basic
types; some prefer the direct definition.<br>
<br>
Yang Ye<br>
<br>
nk yx wrote:
<blockquote cite="midBAY114-F375D8E50CD6CD67D51C806CB5F0@phx.gbl"
type="cite">hi all,
<br>
I am confused about the calculation of non-bonded LJ parameters in
the ffG43a1nb.itp. According to the manual, the combination rule of C6
and C12 is:
<br>
Cij(6)=(Cii(6)*Cjj(6))^0.5
<br>
Cij(12)=(Cii(12)*Cjj(12))^0.5
<br>
However,in the ffG43a1nb.itp file, the values seem not to be in
agreement with the rule. For example,
<br>
O C6=0.0022619536 C12=7.4149321e-07
<br>
OM C6=0.0022619536 C12=7.4149321e-07
<br>
OA C6=0.0022619536 C12=1.505529e-06
<br>
<br>
According to the rule, O OA C6=0.0022619536 C12=(7.4149321e-07
* 1.505529e-06)^0.5 = 1.0565697e-06 but the value is 1.380375e-06 in
the ffG43a1nb.itp.
<br>
In addition, C12 value between O and OM, and tween O and OA should be
the same, but in the file, C12 is 1.38380375e-06 and
2.258907e-06,respectively.
<br>
Could anybody tell me why? Thanks in advance.
<br>
<br>
Regards,
<br>
nkyx
<br>
<br>
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</blockquote>
<br>
<div class="moz-signature">-- <br>
<i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
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