Re: Applying Constraints for ABF Calculations

From: Giacomo Fiorin (
Date: Tue Dec 13 2022 - 12:12:50 CST

Hi Collin, sorry for the late reply.

For preventing the bilayer from deforming, the simpler would be restraining
the atoms near a plane orthogonal to the Z axis using NAMD's "constraints"
keyword (actually position restraints):
and using the "selectConstraints" and related keywords. This should also
achieve the goal of stopping the vertical diffusion of the bilayer.

Other increasingly more sophisticated options would be using a GridForces
potential map to restrain the head groups in select regions:
or using a Multi-Map collective variable, which uses multiple GridForces
maps to quantify the degree of deformation along a specific mode while not
restraining other fluctuations:*sec:cvc_multimap__;Iw!!DZ3fjg!-HPJTLW2J88FJ1mNxrNoF73xNRSlmFPl9sJYwsr23d7QtUHxwy60EagkGcO2teCc-ULgShKUjx9rBbfIsP_HNAwaJA$

The PBC wrapping issue only affects computations like centers of mass or
geometry, where a plain average is taken and there is no robust way to deal
with the periodic images. But distances between those centers are computed
using the minimum-image convention. Since you have a single molecule, it's
all but certain that NAMD will wrap its atoms together and its CoM is well
defined, and as long as the membrane doesn't get close to the top or bottom
of the cell (as you say it is the case) you should be okay.


On Wed, Dec 7, 2022 at 7:54 PM Collin Nisler <> wrote:

> Hello NAMD mailing list, I have two related questions regarding the
> generation of an initial trajectory via SMD to be used in subsequent ABF
> calculations to calculate PMF.
> I want to determine the energy of diffusion of a certain molecule through
> a bilayer. I initially used SMD at 0.2 nm/ns, pulling the center of mass of
> the molecule along z normal to the membrane, with a restoring force on the
> z center of mass of the head groups of the bilayer using SMD and a velocity
> of 0. However, the membrane is very pliable, and it deforms significantly
> such that the molecule's center of mass is below the center of mass of the
> membrane before it even breaks through the surface and enters the bilayer
> (think a very deep bowl shape). I'm assuming this would be a poor initial
> reaction coordinate to obtain the energy of diffusion from, so I'm curious
> if instead would it be viable to constrain the head groups themselves to
> maintain a relatively flat bilayer during the SMD simulation just to
> generate the initial snapshots, but run the colvars relative to the center
> of mass of the membrane?
> Secondly, I see on page 79 of the colvars manual that if a molecule
> crosses the periodic boundary during the run, it could cause complications
> when using wrapall and wrapwater, as I am. If I do what I suggest as
> above and constrain the head groups, it shouldn't be an issue, but as I
> have it now the molecule did jump back to the top of the periodic cell
> before completely exiting the membrane through the bottom. Will this cause
> problems with the ABF calculations? The center of mass of the membrane in z
> does not cross the boundary, only the molecule being pulled.
> Thanks in advance for any help you can provide.
> Collin

This message discusses the usage of Colvars, a software library that is
distributed with NAMD, but is independently developed and maintained.
Please see;!!DZ3fjg!-HPJTLW2J88FJ1mNxrNoF73xNRSlmFPl9sJYwsr23d7QtUHxwy60EagkGcO2teCc-ULgShKUjx9rBbfIsP9f8DD3lw$  for further information.

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