Re: Umbrella sampling-NAMD

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Dec 15 2011 - 11:07:04 CST

Dear Parisa,

The harmonic bias in the colvars module is a Genuine Harmonic
Potential (TM). It does not follow the Silly Non-Standard CHARMM
Convention (TM).
You can see it this way: bond potentials are part of the force field,
hence they have to follow SNSCC (R), whereas harmonic restraints can
be GHPs (R). The tricky thing is that "extrabonds" in NAMD is designed
to work like normal bonds, i.e. CHARMM-style.

The bottom line is, the actual value of the harmonic constant is 100
kcal/mol/A^2. Does that give a PMF that is half-sensible?

Jerome

On 15 December 2011 16:24, Parisa Akhski <Parisa.Akhshi_at_chem.queensu.ca> wrote:
> Dear NAMD experts,
>
> I am using NAMD to run Umbrella Sampling on an ion channel. I am using a
> "harmonic force constant" to keep the ion in the center of bin in each
> window and I know that this value is scaled by the square of the specific
> width as mentioned in the manual. So, if I define "forceConstant=1" and use
> width=0.1, NAMD actually applied K=100 in the calculations.
>
> Then, I am processing the trajectory files by using WHAM to produce PMF. I
> know that WHAM assumes that the biasing potential is V=1/2K(X-X0)^2 whereas
> CHARMM just defines it as V=K(X-X0)^2. This means if I am using K=100 in
> NAMD, I should define K=200 in WHAM.
>
> Since I already have the PMF profile from ABF calculations for the same
> system, I know how the profile should look like and what are the energy
> barriers in my system. Comparing theses results with the ones from Umbrella
> Sampling and WHAM, the shape of the profile makes sense but not the amount
> of the barriers. However, if I change the K value from 200 in WHAM to 50,
> everything makes sense. I double checked this with WHAM experts to make sure
> I am using the correct K (200) in WHAM.
>
> Could you please let me know whether you have any suggestions,... to solve
> this issue?
>
> Many thanks for your time,
>
> Parisa

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:36 CST