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On 12/10/2011 3:48 AM, Yun Shi wrote:
<blockquote
cite="mid:CAHktH26ZuRAtQFxZhCddNTOPrtL_hWmvYL1esyuUFrcvrwP-NQ@mail.gmail.com"
type="cite">Hi Mark,<br>
<br>
I am not quite sure. While the "details" are different, I guess it
is still valid to compare some statistical properties, right? For
example, I should still be able to compare the average COM
distance of these two ligands over long trajectories, and make the
conclusion that one is better than the other since the distance is
smaller. So should I be able to compare any averaged, or say,
clustered properties?<br>
</blockquote>
<br>
It's like comparing a bench experiment done with the same method on
Monday by Bill with one done on Tuesday by Mary. Each of them
stirred their reaction vessel a different number of times under a
different phase of the moon, but if full mixing of the reagents
occurred both times, the results can be compared.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAHktH26ZuRAtQFxZhCddNTOPrtL_hWmvYL1esyuUFrcvrwP-NQ@mail.gmail.com"
type="cite">
<br>
Thanks,<br>
Yun<br>
<br>
<br>
On 11/10/2011 1:40 PM, Yun Shi wrote:<br>
> Hi Justin,<br>
><br>
> I guess you are right, that some processors on that cluster
appear to<br>
> be much slower than others.<br>
<br>
More likely is that the mapping of processes to processors is
faulty, as<br>
Justin said.<br>
<br>
><br>
> But I am still wondering that, would the difference in
initial maximum<br>
> inter charge-group distances (0.451 nm vs 0.450 nm) and
minimum<br>
> initial size of DD gird (0.620nm vs 0.618nm) make the two
simulations<br>
> NOT comparable? Because I want to compare the interactions of
two<br>
> different ligands with the same protein.<br>
<br>
That's just a detail of how the simulation is being implemented in<br>
parallel. There are a vast number of algorithmically equivalent
ways to<br>
do this, and the initial conditions determine which is chosen.
Since<br>
your initial conditions differ, so do the details.<br>
<br>
Mark
<br>
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