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On 18/12/2011 7:41 PM, Saba Ferdous wrote:
<blockquote
cite="mid:CANTGNo4Ri6M5BL94KZvPPsGpcUZCV3+40wyy_n0owfPnNWChuQ@mail.gmail.com"
type="cite"><br clear="all">
<div><span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Dear
Gromacs experts,</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">I
want to ask about coulomb energies. Like if coulomb-SR and
coulomb-14</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">show
high RMSD then what should we interpret from such results??</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
</div>
</blockquote>
<br>
Nothing. The fact that it is convenient to compute and report those
terms separately doesn't mean there's any connection with a useful
observable. Force fields are parametrized to reproduce some
experimental and/or computational data. There's no a priori reason
to suppose that bits and pieces of the force field in isolation have
any particular connection to any such observable.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CANTGNo4Ri6M5BL94KZvPPsGpcUZCV3+40wyy_n0owfPnNWChuQ@mail.gmail.com"
type="cite">
<div>
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"> Average
Coulomb Energy (kJ/mol)</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">-1.62657e+06</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">RMSD</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">2236.85</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Error
Estimation</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">150</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Total
drift (kJ/mol)</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">-894.82</span><br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<br
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span
style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">Many
thanks</span>
</div>
-- <br>
Saba Ferdous
<div>Research Scholar (M. Phil)</div>
<div>National Center for Bioinformatics</div>
<div>Quaid-e-Azam University, Islamabad</div>
<div>Pakistan</div>
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