Re: Problem with Methane-Methane PMF

From: Shaon Chakrabarti (
Date: Sat May 12 2012 - 13:46:01 CDT

Dear Giacomo and Aron,
Thanks a lot for the nice and detailed explanation of the physics...I've
made the changes and
everything's ok now. I guess I should've worked through the derivation of
the ABF
method first before applying it, to understand what the hideJacobian option

Thanks again for the help,

On Fri, May 11, 2012 at 2:40 PM, Giacomo Fiorin <>wrote:

> 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
> place.
> 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
> calculation.
> Bests
> Giacomo
> 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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