On 12/10/2011 3:48 AM, Yun Shi wrote:
Hi Mark,
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?
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.
Mark
Thanks,
Yun
On 11/10/2011 1:40 PM, Yun Shi wrote:
> Hi Justin,
>
> I guess you are right, that some processors on that cluster appear to
> be much slower than others.
More likely is that the mapping of processes to processors is faulty, as
Justin said.
>
> But I am still wondering that, would the difference in initial maximum
> inter charge-group distances (0.451 nm vs 0.450 nm) and minimum
> initial size of DD gird (0.620nm vs 0.618nm) make the two simulations
> NOT comparable? Because I want to compare the interactions of two
> different ligands with the same protein.
That's just a detail of how the simulation is being implemented in
parallel. There are a vast number of algorithmically equivalent ways to
do this, and the initial conditions determine which is chosen. Since
your initial conditions differ, so do the details.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
