Problem with Methane-Methane PMF

From: Shaon Chakrabarti (
Date: Fri May 11 2012 - 16:08:23 CDT

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
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
    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
    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

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

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,

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