[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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users