VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 25 2018 - 07:43:40 CDT

Hi Kelly,

as in Umbrella Sampling, the setup process you are describing is entirely
independent from the free energy calculation itself. In ABF that is not
necessary in principle: if you define a broad range for ABF to sample, as
in your example, a single ABF simulation will eventually sample this range
by continuous diffusion. However, this can be made faster by creating a
small number of windows - it could be just cutting your range in half,
which means setting up one second copy of your system at a different
position.

Some ABF users have applied steered MD for preparing a series of starting
points, but that comes with the usual caveat: watch out for non-equilibrium
effects that the system might remember through the ABF simulations.

Jerome

On 24 May 2018 at 19:10, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> I am preparing to do some ABF calculations with the molecules I sent
> through FFTK by working through the tutorial. I am placing these molecules
> in the influenza A M2 protein to get their free energy profiles in order to
> understand their entry/exit and interactions inside the protein. I will
> have some questions as I work my way through the tutorial. My first one
> is more of a general question on how ABF works. I've done some umbrella
> sampling before, and the way we have done this in the past is create
> multiple input files with the molecule/drug at different positions in the
> protein, delete the waters at the drugs new position, and submit all of
> those jobs to the supercomputer, which as you can imagine is very
> tedious/inefficient. I am wondering though how the ABF set up in NAMD
> handles moving the drug and deleting waters around the drug at the new
> position? For example, say I have the drug starting at one end of the
> protein and we call that position on the reaction coordinate -15 Angstroms,
> and the drug is to be moved to the other end of the protein, call it 15
> angstroms (so, 30 angstroms for the total reaction coordinate), how
> does the part of the colvars script, (width 0.1, lowerboundary -15,
> upperboundary 15), move the drug to the next spot and delete waters around
> it? Is this some kind of a loop that NAMD recognizes to move the drug?
> Thanks!
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
>