From: Chris Chipot (chipot_at_illinois.edu)
Date: Thu Aug 26 2021 - 02:41:52 CDT
Ishaan,
there are a number of quantities that you ought to look into. First, you
should histogram the difference between the extended variable and the
actual variable (from your *traj* file), and ascertain that it obeys a
normal law. Second, you should make sure that your bias is properly
applied, that is past a threshold (fullSamples) of accrued force samples
guaranteeing minimum non-equilibrium effects. Third, you should make
sure that your distanceXY component is correctly defined, with the
desired subsets of atoms.
Regards,
Chris
On 8/26/21 12:28 AM, Ishaan Roy wrote:
>
> Hi Peter,
>
> Nothing stands out as weird about the runs, visually or otherwise. The
> sampling distribution is, I believe, as one would expect, generally
> increasing for higher values of the coordinate and the trajectory
> follows a square-root diffusion trend. There’s no sign of the protein
> getting stuck anywhere.
>
> Thanks,
>
> Ishaan
>
> *From: *Peter Freddolino <mailto:petefred_at_umich.edu>
> *Sent: *Wednesday, August 25, 2021 10:34 PM
> *To: *<namd-l_at_ks.uiuc.edu> <mailto:namd-l_at_ks.uiuc.edu>; Ishaan Roy
> <mailto:royi_at_uchicago.edu>
> *Subject: *Re: namd-l: Unrealistically High Keq in eABF Seperation
>
> Dear Ishaan,
>
> If your simulations haven't yet converged, there is really no sense in
> evaluating the energies completely yet. With that said, how is the
> sampling looking across the different values of your reaction
> coordinate? Is the reaction coordinate stuck somewhere or is the
> system diffusing freely along it?
>
> Have you visually inspected your system to make sure nothing weird is
> happening?
>
> Best,
>
> Peter
>
> On Tue, Aug 24, 2021 at 7:08 PM Ishaan Roy <royi_at_uchicago.edu
> <mailto:royi_at_uchicago.edu>> wrote:
>
> Hello,
>
> I am using eABF to separate two membrane proteins to find the free
> binding energy. The PMF values produced in my runs seem to be
> incredibly high compared to consistently reaching the 100s order
> of magnitude. We haven’t completed a run that plateaus in free
> energy yet, but this is an example showing what the PMF looks like.
>
> A maximum PMF this high already produces a value for the binding
> constant that is on an order beyond 10^100. Besides being high, it
> might be worth mentioning that the nonbonded energies are very
> close to 0 near the end of this run, but the PMF gradient doesn’t
> level off at all. Any ideas on what might be causing this? Or is
> such a value plausible? This only seems to be a problem with the
> separation runs; my other colvars produce PMF plots that are
> closer to what I’ve seen.
>
> Thanks,
>
> Ishaan
>
--
Chris Chipot, Ph.D.
CNRS research director, University of Lorraine
Adjunct professor of physics, University of Illinois, Urbana-Champaign
_______________________________________________________________________
Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
3161 Beckman Institute for Advanced Science and Technology
University of Illinois at Urbana-Champaign
405 North Mathews
Urbana, Illinois 61801 Phone: (217) 244-4361
E-mail: chipot_at_illinois.edu
Christophe.Chipot_at_Univ-Lorraine.fr
Web: https://physics.illinois.edu
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