Re: Umbrella sampling-NAMD

From: Aron Broom (
Date: Thu Dec 15 2011 - 14:14:05 CST

I guess there might be two things to check for the umbrella sampling:

1) you need to remove any data at the start of each window that represents
the system equilibrating to that new force constant. If you've started
each window from the end of the previous window, and the change in your
reaction coordinate for each window is small, then this probably doesn't
amount to much, but it could still be worth removing, at it might be giving
a systematic error to each window. If the equilibration time is short
compared to your window simulation time then this likely won't matter much.

2) Have you ensured that the data being used by WHAM has had
auto-correlations removed? Normally people just record the value of the
reaction coordinate say every 2000 fs or something (depending on the type
of system) and then use all the values as input for WHAM, but you should
really check your reaction coordinate trajectories within each window and
see how long it really takes for your system to lose auto-correlation.
Then, you should trim down the data until you have no auto-correlation.
WHAM assumes that each value it is binning into the histogram for each
window is an independent value, which is only true if you've given it a
long enough time between each recording of the value. If you do this you
may find that a number of your windows suddenly become very sparse on data
and the error becomes quite large.

Even if attending to the above issues doesn't change your result, at least
it will allow you to use WHAM to accurately estimate the error.


On Thu, Dec 15, 2011 at 1:51 PM, Parisa Akhski <> wrote:

> **
> Thanks Aron for your comment,
> Yes, I have checked the convergence of ABF results and they are OK. For
> umbrella sampling the only criteria I know to check is the overlap between
> windows which is OK. Is there anything else I could check for US to make
> sure it has converged?
> Many thanks,
> Parisa
> -----Original Message-----
> From: Aron Broom [ <>]
> Sent: Thu 12/15/2011 12:11 PM
> To: Parisa Akhski
> Cc:
> Subject: Re: namd-l: Umbrella sampling-NAMD
> Parisa,
> If you had a very simple system like two molecules in the gas phase then I
> would be worried by the disagreement between Umbrella Sampling and ABF, but
> given the complexity of your system, are you sure that the ABF calculations
> have given an accurate PMF? Have you checked that doubling the sampling
> parameter and/or doubling the simulation time has no effect on your ABF
> PMF? I would intuitively suspect that the difference is because one of
> your analysis methods has not really converged properly.
> ~Aron
> On Thu, Dec 15, 2011 at 10:24 AM, Parisa Akhski <
>> 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
> >

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