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Hi Jie-rong--
>
> Thanks a lot for your reply.? I didn't analyze the radius of gyration of
> "*_ave.pdb", but all the others.? Calculations were performed 100 times and 50
> with lowest energies were analyzed.? That is, with Ne = 1, 50 pdb files, with
> Ne = 8, 400 pdb files were analyzed.? The Rg of 50 (or 400) structures were
> averaged.? I still don't get why the results without restraints are different
> in different size of ensemble......
what Rg values do you get for the Ne=8 and Ne=1 calculations?
>
> Is that possible to use XplorPot ("BOND",...) instead of AvePot(XplorPot,
> "BOND",...) in ensemble calculation (for Ne > 1), if I don't want these terms
> to be averaged across the ensemble members? ??
>
Practically, this will not work. Anyway, there must be a single sum
energy to perform minimization and dynamics.
I suspect that a difference in Rg of this unrestrained system is due to
different effective temperatures- due to ensemble averaging of kinetic
energy. This might be tested by increasing the Ne=8 temperature.
The bottom line is the goal of your simulated annealing calculations: it
should be to optimize some target energy which includes restraints, and
the results should be rather insensitive to protocol parameters, such as
temperature - otherwise you have an extremely underdetermined system. In
that case, more of a modeling calculation might be appropriate - using a
realistic description of the solvent and realistic temperatures.
I hope this helps--
Charles
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