AMBER Archive (2008)

Subject: Re: AMBER: B-factor calculation from data with different write frequencies

From: Sally Pias (sallypias_at_gmail.com)
Date: Tue May 27 2008 - 22:42:13 CDT

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_at_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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu