Targeted MD and the MARTINI Coarse-Grained Force Field

From: Fotis Baltoumas (
Date: Fri Feb 06 2015 - 10:06:55 CST

Dear NAMD users,

I've been trying to study the effects of specific structural movements
upon a transmembrane protein system using Targeted MD. However, the size
of the system (multiple chains forming a complex, exomembrane domains
present, large lipid bilayer etc) makes simulation difficult. Therefore, I
was thinking of using NAMD's Martini implementation to coarse grain the
system and perform TMD for the RBCG model.
First of all, in your opinion, does that make sense? Would TMD work for a
CG force field such as MARTINI in the manner it would do for a standard
atomistic one?

If I do combine the two, what should I keeping mind when setting a value
for the k constant? So far I've been using 200 kcal/mol/angs.^2 for
all-atom TMD, as suggested in the manual, however I'm not sure whether
that same value would be
appropriate for a coarse grained simulation. Also, Coarse-Grained
simulations tend to give larger RMSD values than the ones obtained through
all-atom ones, due to the rough nature of the force field. Since in TMD
RMSD is used to calculate the steering forces, how does this difference
between CG and atomistic RMSDs factor into the process?

I would be interested in reading your thoughts on the matter.

Thank you in advance,

Fotis Baltoumas

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