Re: Problem with Methane-Methane PMF

From: Giacomo Fiorin (
Date: Fri May 11 2012 - 16:40:03 CDT

Hello Shaon, is the distance PMF defined in the same way between umbrella
sampling and ABF?

Strictly speaking, the free energy of interaction between the methane
molecule no. 1 and methane molecule no. 2 go down with the distance, and is
not limited. The reason why, is that the density of states for a given
distance d is proportional to the area of the sphere with radius d: 4 pi
d^2. Higher and higher density of states -> lower and lower free energy.

The only reason why the "correct" result is when PMF levels off, is that by
convention we take into account that there is a finite concentration of
solute. So, even though methane no. 2 falls down a decreasing curve and
leaves methane no. 1 forever, methane molecule no. 3 comes and takes its

In ABF, this "leveled off" definition of the PMF can be controlled by the
hideJacobian option. Did you leave the default or use it?

In umbrella sampling, you will control this when you do the WHAM


On Fri, May 11, 2012 at 5:08 PM, Shaon Chakrabarti <> wrote:

> Dear NAMD experts,
> I am running into a problem while computing the Methane-Methane PMF
> using NAMD (Umbrella Sampling and then WHAM). After the contact minimum
> and solvent separated minimum, the PMF should level off, but the PMF I'm
> computing
> just keeps decreasing instead of becoming almost constant! I have just not
> been able to
> figure out the problem, and would be really grateful for any ideas.
> I am using an all atom representation of methane, and TIP3 water. I am
> using a
> 2fs time-step and have a 12 Angstrom cutoff for non-bonded interactions.I
> have periodic
> boundary conditions,PME and wrapAll switched on. For the harmonic biases,
> I am using
> the Colvars module in NAMD. I minimize for 20000 steps, then equilibrate
> the system
> (without any bias) for 1ns, after which I use the various biases to
> generate sampling. All
> of this is at 300 K temperature.
> 1) I have tested my WHAM code with other codes available on the web
> (including
> Alan Grossfield's code). All of them give the same wrong result. Hence
> I am almost
> certain that the mistake is not in the WHAM portion, but in generating
> the
> trajectories using NAMD.
> 2) I have tried using water boxes of side varying from 32 angstroms to 44
> angstroms. Every
> time I get the same problem.
> 3) I used a variety of spring constants--1,2,6,8 kcal/(mol.A^2) to get
> varying degrees of overlap
> of the histograms. I have also tried placing the harmonic centers at
> different separations, but
> to no avail.
> 4) I have tried using 5000 steps (10000 fs) for decorrelation, and 40 ns
> trajectories for sampling.
> Increasing decorrelation time and sampling time doesn't change the
> results.
> 5) I have used ABF to recompute the PMF--that does give CORRECT results.
> So I guess I'm not
> committing any stupid error while building the methane-methane+water
> system.
> At this stage I'm really at a loss about the source of this problem. It
> would be of immense
> help if someone could point out where I'm making a mistake.
> Thank You,
> Shaon

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