Re: distanceZ - harmonic restraints

From: Narasimhan LOGANATHAN (
Date: Mon Mar 18 2013 - 13:38:55 CDT

Hi,  Thanks for the reply. I would do the constraints according to both of your suggestions.Also, I will update on my progress.

Aron Broom <> wrote:I was writing something but Jerome responded first with more or less what I was going to say. 

Just for more detail, for the distanceXY constraint (which you can define using the same definitions you made for distanceZ), you can set the harmonic forceConstant to 0, but, have an upper and lower boundary/wall with an appropriate force constant.  In this way your ion will explore a cylinder.  I wouldn't give a forceConstant to this distanceXY constraint, because then you are making some very specific assumptions about the path the ion uses, rather than letting it find the lowest free energy path within that volume.

One other little point:  since you're planning to do umbrella sampling, it might make sense for simplicity's sake (to save yourself a potential headache later on) to set the colvar width to 1.0.  Otherwise when you enter your force constant for analysis with something like WHAM, you're going to have to divide (multiply?) the force constant you specified by the colvar width.  You can see this in the manual, but basically, unless you are doing something like metadynamics or ABF you should just set the width to 1.0, your actual PMF resolution will be determined when you perform the analysis in WHAM.


On Mon, Mar 18, 2013 at 1:14 PM, Narasimhan LOGANATHAN <> wrote:
Hi all,
       I am using collective variable analysis module in NAMD to get PMF profile.
I am quite new to collective variable analysis module in NAMD.
I am trying to calculate the free energy profile of an ion along the normal to specific site (COM of six atoms) on a solid substrate.
Hence, i used distanceZ component (Projection of a vector to an axis)for the CV analysis method using harmonic constraints.
Below is the configuration file i used for CV module. The simulations runs fine and i have the PMF.

CV module
colvar {

name                         pmf-dist
width                        0.2
lowerboundary                1.0
upperboundary                15.0
expandboundaries             off

       distanceZ {

            main {
              atomNumbers  1512
            ref {
             atomNumbers  1375 1467 1406 1385 1384 1396
            axis {
              (0.0, 0.0, -1.0)
      forceNoPBC             no
      oneSiteSystemForce     no
outputValue                 on
outputVelocity              off
outputSystemForce           on
outputAppliedForce          on

      harmonic {
          name              umbrella
          colvars           pmf-dist
          forceConstant     2.0
          centers           8.0
However, when i try to view the trajectory files(*.dcd), the results are quite different.
For instance, the distance between the main and ref group is fine on Z -axis.
However, during the course of the simulation, the vector moves along the XY plane at the centered Z-position.
I understand that only the Z component is constrained and not XY.

My doubts are
1) why the vector is moving along the XY plane when the axis keyword for x and y are set to be 0.0
2) Since, there is a constant movement along the XY plane, does it still hold the atom identities for distance measurements.
3) I think that this motion has a strong influence on sampling the regions specific to the defined sites.
4) how to avoid this and to keep the XY motions to minimum and to have calculate the PMF for the specified sites on the substrate.

Could you please help me in this regard

Thanks in advance


Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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