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On 19/09/2011 1:13 AM, Gideon Lapidoth wrote:
<blockquote
cite="mid:CAB7OWN-TXnEu0-vD9cEHF6XOz9rkbyvN-438m+_fG-_ZF_R_OA@mail.gmail.com"
type="cite">
<div dir="ltr">Hi all,
<div><br>
</div>
<div>I ran g_energy in order to calculate the LJ energy between
a pip2 (<span class="Apple-style-span" style="font-family:
sans-serif; line-height: 31px; background-color: rgb(255,
255, 255); ">Phosphatidylinositol 4,5-bisphosphate) molecule</span> and
the solvent using GROMACS 4.0.7. the pip2 molecule is very
polar and the avg. coulomb energy value I got between the
ligand and solvent was ~ 3100 KJ.</div>
</div>
</blockquote>
<br>
An equilibrated condensed-phase system of mixed positive and
negative charges using a normal biomolecular force field should have
negative Coulomb PE.<br>
<br>
<blockquote
cite="mid:CAB7OWN-TXnEu0-vD9cEHF6XOz9rkbyvN-438m+_fG-_ZF_R_OA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div> The solvent includes water molecules and Cl and Na ions to
counter the pip2 charge. the production run was done in npt
conditions. the total charge of the pip2 molecule is -6 e. The
avg. LJ energy I got was ~190 KJ. </div>
<div>I am trying make sense of this. could it be that the polar
interactions between the solvent and ligand are so strong that
they can influence a positive LJ energy? </div>
<div>Does anyone have any idea why this could be ? <br>
</div>
</div>
</blockquote>
<br>
Force fields are parameterized to reproduce certain experimental or
computational results, in the hope that such reproduction will
permit simulations using that force field to sample similar chemical
ensembles with correct frequencies. They're not parameterized such
that the absolute values of any energies or energy components means
anything, and one has to work hard to demonstrate anything sensible
about energy differences, too. What were you hoping to observe?<br>
<br>
Mark<br>
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