Re: distanceZ - harmonic restraints

From: Aron Broom (
Date: Mon Mar 18 2013 - 12:35:47 CDT

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
> }
> Constraints
> 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
> Sincerely,
> Naresh

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

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