Hi,
On Wed, Dec 11, 2013 at 11:18 AM, filip fratev <filipfratev.yahoo.com>wrote:
> Hi Jason,
> Thanks for your answer, now it is much clear! What I worry about is the
> units in amd.log. As Dan have already mentioned in this topic:
> http://archive.ambermd.org/201304/0257.html
> "I believe that the potential/dihedral energies are reported in units
> of kcal/mol, but the boost energies are reported in units of KT."
>
> Is that correct? and also is that the reason for problems described here
> by Alonso?:
> http://archive.ambermd.org/201304/0275.html
Yes to both; boost energies are reported in KT specifically to make
reweighting simpler.
-Dan
>
>
>
> Regards,
> Filip
>
>
>
>
> On Wednesday, December 11, 2013 7:55 PM, Jason Swails <
> jason.swails.gmail.com> wrote:
>
> On Wed, Dec 11, 2013 at 10:56 AM, filip fratev <filipfratev.yahoo.com
> >wrote:
>
> > Hi all,
> > Recently I asked about the progress of the aMD tutorial and the python
> > script to reweight and plot the energies. Is there any progress?
>
>
> Not to my knowledge. I think the people originally responsible for the aMD
> implementation have moved on and may not be as regular contributors
> anymore, so I'm not sure what the status of this is.
>
>
>
> > I think that there are still some open questions, which not received
> clear
> > answer for me:
> > http://archive.ambermd.org/201304/0277.html
> > http://archive.ambermd.org/201304/0307.html
> >
> > May ask for some very simple guide about reweighting procedure? I'd like
> > one of my students to make some python script but want to be sure that
> use
> > the correct formula and approach.
>
>
> The formula for reweighting can be found in the original aMD paper, though.
> You would just need to find the weight for each point (using the output
> from the aMD log). numpy provides an option to supply point weights in the
> 'histogram' function, which seems about as straightforward as possible.
> You could, of course, implement this in pure python, but numpy will be
> much faster.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Dec 11 2013 - 11:00:02 PST
