RE: Umbrella sampling-NAMD

From: Parisa Akhski (
Date: Fri Dec 16 2011 - 09:29:27 CST

Hi Chris,

Thanks very much for your e-mail.

I have already seen your previous discussion in the mailing list. K=100 dose not produce the expected results.

Here are the issues I am running to:

1. According to the user manual:

forceConstant < (harmonic) Harmonic force constant (kcal/mol) >
Acceptable Values: positive decimal
Default Value: 1.0
Description: This defines the constant for the harmonic potential. To ensure consistency
for multidimensional restraints, it is scaled by the square of the specific width for each colvar
involved (which is 1 by default), so that all colvars are internally rendered dimensionless and
of comparable size. For instance, a force constant of 10 kcal/mol acting on a dihedral colvar
with a width of 2 degrees will amount effectively to 2.5 kcal/mol×degree-2.

In my previous e-mails I was thinking that NAMD ALWAYS scales K. But, now I see that the reason to scale K is to fix the dimensions in multidimensional harmonics. Now, my understanding is that for 1D (applying harmonic on one colvar) NAMD does not scale K since it already has correct dimensions. For 2 and 3 colvars, it scales accordingly. Is this correct? If so, I am using K=1 and I only have one colvar (1D) so NAMD applies K=1. This tells me that I have to use K=2 in WHAM which gives me very small energy barriers and very far from my expectations.

In response to Jerome's question, going from K=200 to K=100 and K=50 produces PMF with half and one-fourth height, respectively. But, for smaller values of K (K=2) the dependence is not linear.

2. Number of bins in WHAM: I am still not clear how to choose the "number of bins" in "WHAM"? My results are highly dependent on this parameter especially when the force constant is high (K=200). How should I decide on the "number of bins" in "WHAM"?



-----Original Message-----
From: Chris Harrison []
Sent: Thu 12/15/2011 3:07 PM
To: Parisa Akhski
Cc: Aron Broom;
Subject: Re: namd-l: Umbrella sampling-NAMD

Please refer to Jerome's response as it is absolutely correct, and has
been previously discussed on the namd-l list. I explicitly remember
answering the same questions less than 2 months ago.

So as Jerome asked, how does the profile look when WHAM is used at K=100?


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                          Voice: 773-570-0329              Fax:   217-244-6078
Parisa Akhski <> writes:
> Date: Thu, 15 Dec 2011 13:51:57 -0500
> From: Parisa Akhski <>
> To: Aron Broom <>
> CC:
> Subject: RE: namd-l: Umbrella sampling-NAMD
> 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
> >

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:04 CST