Bill,
Thank you for the helpful suggestion. I thought of something like
this also, but will I be sacrificing "quality" of the B-factor
calculation due to reduced MD sampling? Also, I have conducted an
independent simulation of the same molecule with no ligand bound
(first simulations were with bound ligand) and with ntwx = 250. Will
I need to select every other frame from this trajectory as well, in
order to make the data sets comparable?
Thanks,
Sally
On Tue, May 27, 2008 at 10:44 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> ntwx = 100 for the first 2.5 ns
>> ntwx = 250 for another 5 ns.
>
> Solution: select every 5th frame from the 1st 2.5 ns and every other
> frame from the next 5 ns, then merge the two selected trajectories.
>
> Bill
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Received on Wed May 28 2008 - 06:08:02 PDT
