Hi,
On Wed, Aug 7, 2019 at 7:58 AM Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
>
> Assuming the data subsets match well, you can convert the histogram bins to
> free energy by using a script that calculates
> -RTln(Pi/P0)
> where Pi is the population in bin at coordinate value i and P0 is the
> population of the most populated bin. This sets the minimum free energy at
> 0 (which is arbitrary).
Quick note: the 'free <temperature>' keyword of the cpptraj 'hist'
command will do this for you automatically using the specified
temperature. See the manual for full detail.
-Dan
>
> Next you can repeat this for your data subsets to calculate the
> uncertainties in the free energy values. Don't neglect this part, or you
> may generate very misleading data if the populations are not converged. I
> microsecond may be enough, or it may be far too short. It depends on your
> system and the timescale of the motions along the coordinate you selected.
> This is why viewing the time dependence of the calculated coordinate values
> is important.
>
> On Tue, Aug 6, 2019, 11:18 PM M RCC <mkr3j2c1.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I have performed amber simulation for 1 microsecond using pmemd module. I
> > want to generate free energy landscape from the trajectory. Is there any
> > software tools/tutorials /protocols available for this?
> >
> > (I have generated in Gromacs trajectory, But no tutorials are available for
> > this in Amber)
> > Thank You
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> >
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Received on Thu Aug 08 2019 - 05:30:02 PDT
