Hello,
Without looking at the trajectory, the results seem fine to me.
Your PMF goes from 0 Angstroms to 30 Angstroms on the X-axis, and
reproduces the 0 Angstrom to 30 Angstrom half of the example plot pretty
closely.
You will need to calculate the -30 Angstrom to 0 Angstrom half of the PMF
if you want a full comparison.
You can combine the restart files for all of your windows into a trajectory
and visualize them to look at the system.
Good luck,
Christina
On Thu, Mar 27, 2025 at 2:38 AM SANKAR MAITY via AMBER <amber.ambermd.org>
wrote:
>
>
> Dear AMBER Community,
>
> I am performing umbrella sampling following the tutorial available at [
> https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial | this
> link ] . My objective is to determine the free energy profile for the
> transfer of an ethanol molecule through a DMPC membrane bilayer. My system
> is similar to the tutorial, except that I have replaced methanol with
> ethanol while keeping the number of DMPC molecules and the box dimensions
> unchanged.
>
> I followed all the steps as outlined in the tutorial. I generated 32
> windows with 1 Å spacing and ran each window for 5 ns. After running WHAM,
> I observed that the PMF values suddenly increased after the 7th window,
> reaching unexpectedly high values up to the 32nd window. The histogram
> distribution appears satisfactory, but after applying diffusion correction,
> I obtained a PMF with negative values. I have attached all the plot.
>
> I am unsure what mistake I might have made. Could anyone suggest how to
> resolve this issue?
>
> Thank you in advance.
>
>
>
>
> Best regards,
> Sankar Maity
> Research Scholar
> NIT Rourkela
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-----------------------------------------------------------------
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Thu Mar 27 2025 - 06:00:02 PDT
