SMD restraints

From: Allen, Caley R (
Date: Mon Nov 14 2016 - 15:14:09 CST

Greetings NAMD experts.

I was browsing through the mail list, in an effort to find a solution to a problem when I stumbled upon a post from Feb. 29, 2012. The interesting part (to me) reads as follows (Axel wrote the response in black):

What you say makes sense, but I want to compute the work done by the pushing
no. this is bad. you cannot change the force field.
force as I insert the peptide into the membrane (steered MD). Hopefully I'll
get some free energy profile as a function of insertion depth. Hence I need
the membrane to stay in place.
not quite. what you need is to have the steering force
being applied to both, the center of mass of the *entire*
membrane and the center of mass of the *entire* protein.
restraining a few lipid molecules in space will not help.
best case, it will artificially bend the membrane, worst
case, it will just rip those out.
in general, you should not worry too much about a little
drift, after all you have periodic boundary conditions,
and for a clean steered MD PMF on inserting a protein
into a membrane, you need quite a bit of water in between.

I am attempting to do something very similar – I would like to “pull” a ligand off of the bilayer leaflet via SMD at a constant velocity. I choose a steering atom in the ligand and an “anchor” atom in a lipid in the bilayer. And the result was an impressively significant bending of the bilayer. It was pointed out in the passage above to use “the center of mass of the *entire* membrane, and the center of mass of the *entire* protein”.

My question is how; how do you make the selection for the “center of mass for the entire membrane/protein”?

NAMD’s implementation of tcl is limited. For example currently in the smdforces.tcl script I make the atom selections for the force application as follows:

set id1 [atomid A 1 CA]
set grp1 {}
lappend grp1 $id1
set a1 [addgroup $grp1}

Then similarly for id2.

Would using colvars be a solution?

I am unfamiliar with colvars, so any examples and/or guidance is much appreciated.

Cheers and Best Wishes,
C. Allen

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