From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Aug 16 2016 - 12:25:06 CDT
Hi Sachin,
Do you have wrapall turned on? To me this looks like perfectly normal membrane simulation, except that randomly you have net momentum in the top and bottom leaflets that aren't equal (which happens alot! System momentum being zero doesn't mean the component momenta are). Usually, this is hidden by the fact that wrapall on will rewrap lipids as they drift automatically. This can also be fixed by postprocessing in vmd (see pbctools and its wrap command). In short, your dynamics are probably fine, it just looks a little funny when viewed. The one caveat I need to add to my statement is that you didn't specify if your barostat is set to have a constant ratio or not. Membrane and water hav different compressibility moduli, so you can't use the standard isotropic barostat.
Happy Membraning!
-Josh
On 08/16/2016 11:04 AM, Sachin Natesh wrote:
Hello,
I am simulating peptides above a lipid bilayer in the NPT ensemble. After ~200ns of production, the membrane layers appear to undergo in-plane shearing (in the unwrapped trajectory, see links for screenshots). My periodic boundary conditions minimize the x/y distance between images, so the membrane is 'infinite' in the x-y plane. The only deformation is the inter-layer shear and fragmentation at the edges of the membrane (see link for membrane w/ multiple periodic images).
Has anyone observed this behavior for similar systems? Might this be an artifact of unwrapping, or improper handling of image centering?
Any help is appreciated!
Thanks,
Sachin Natesh
https://www.dropbox.com/s/i1rlm0zm7zki46l/after.png?dl=0
https://www.dropbox.com/s/313ywglb0mghlzw/before.png?dl=0
https://www.dropbox.com/s/h60m05g6akt9n7z/top.png?dl=0
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