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On 7/04/2011 9:23 AM, Elisabeth wrote:
<blockquote
cite="mid:BANLkTimwzcGHnecDU0FXWpB0kqHGU1TZeA@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On 6 April 2011 15:01, Michael
Brunsteiner <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:mbx0009@yahoo.com">mbx0009@yahoo.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
Elisabeth,<br>
<br>
You CAN, in fact calculate the contribution of the reciprocal
part<br>
of the PME energy to the binding energy between two components
in<br>
a heterogeneous system, its just quite tedious...<br>
say, your system is molecules A and B for which you want to
know<br>
the interaction energy, and the rest of the system, typically<br>
the solvent, we call C.<br>
Now your total Reciprocal Coulomb energy will have six parts:<br>
ER_tot = ER_AA + ER_BB + ER_CC + ER_AB + ER_AC + ER_BC<br>
but these parts are NOT given in the gromacs output as they<br>
cannot be calculated DIRECTLY, you have to calculate<br>
them by setting the charges on A, B, or C (or combinations
thereof)<br>
to zero (there is a tool for setting the charges in a tpr file<br>
to zero) and then do more runs with: "mdrun -rerun" based on
the<br>
original trajectory to get the required contributions.<br>
<br>
then E_AB = ER_C0 - ER_A0C0 - ER_B0C0<br>
<br>
(or something like it, do double check that formula, i can't
be bothered<br>
thinking it through now ... here ER_A0C0, for example, is the
reciprocal<br>
part of the coulomb energy with charges in groups A and C set
to zero, etc)<br>
<br>
this being said ... it's tedious, time-consuming, and
error-prone<br>
(you need to use double precision and save a lot of frames to<br>
get reasonably accurate numbers)<br>
</blockquote>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">You might be better off using reaction
field, or PME and simply<br>
ignore the reciprocal part altogether (if your molecules A, B<br>
are NOT charged and have no permanent and large dipole moment<br>
you might get away with the latter)<br>
<br>
</blockquote>
<div>Thanks for your elaborate message. <br>
<br>
The point is in my case there is no option other than ignoring
LR since LR is not covered by shift or switch functions but at
least what PME reports for SR is more accurate. So the
decomposed Coulmb. SR terms I am getting using energy groups
from PME are "reliable ?<br>
</div>
</div>
</blockquote>
<br>
The short-range interactions with PME are no longer a 1/r function.
See manual section 4.9.1. By design, the modified function decays to
zero faster. Whether your observable is perturbed by using any of
these modified short-ranged approaches is probably unknown.
Conventional wisdom would be that they were all flawed from lack of
the long-range contribution.<br>
<br>
Mark<br>
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