[gmx-users] Deformation of monomer in pulling simulation

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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