[gmx-users] Deformation of monomer in pulling simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 18 22:52:37 CEST 2011

Robert Dole wrote:
> Hello all,
> I'm trying to pull two peptides (coordinates are from their dimer 
> crystal structure) apart using the distance option for the pull geometry 
> and harmonic potential using GMX 4.5.3 using OPLS-AA to define the 
> protein and tip3p for the water model with NaCl used @ 140 nM for ions. 
> The box is 20 nm long and the pulling is done along the longest axis of 
> the cuboid (i.e., Z-direction) such that the peptide move much less than 
> half the periodic distance of the box over the course of the simulation. 
> I've run the pulling simulation at 0.0005 and 0.001 nm/ps and with 
> pull_k1 set to 1000 or 5000 to qualitatively see whether a higher force 
> constant made a difference (which is doesn't).
> As the simulation runs, there is a large deformation of the monomer 
> being pulled in which the pulled peptide (initially looks like a "V" 
> with the hydrophobic core in the "middle") is stretched. The hydrophobic 
> N-terminal stays very close to the reference peptide for the majority of 
> the simulation until it finally comes "off" towards the end of the pull run.
> I've gone through some of the literature and it seems as though this is 
> an expected phenomenon (i.e., deformation of the pulled structure), but 
> the deformation is so severe in my case, that it loses ~25-35% of its 
> secondary structure! Any suggestions as to how I can remedy this? I 
> thought of using distance restraints on the pulled peptide for the 
> pulling simulation after which I would remove them for simulations of 
> the windows, but I thought I would ask before trying this as I've nearly 
> reached my monthly quota on the HPC cluster I work on.

I've done this to preserve secondary structure content before.  Distance 
restraints between C-alpha atoms work nicely, though they require you to use 
particle decomposition, so the runs are somewhat slower.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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