Applying Constraints for ABF Calculations

From: Collin Nisler (
Date: Wed Dec 07 2022 - 18:47:54 CST

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.


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