From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Aug 16 2016 - 13:06:52 CDT
Well, your protein will move too. I like measuring contacts, so what I do is just center the trajectory on the protein (pbc wrap -all -center com -centersel "protein") and script everything so I can make the measurements I want in an automated way.
On 08/16/2016 12:01 PM, Sachin Natesh wrote:
Thanks for your response. The screenshots I provided are from the unwrapped trajectory. As you suggest, the membrane looks fine when wrapped. The barostat was set to have constant ratio. Our goal is to study protein-lipid interaction. For this purpose, does it suffice to unwrap the protein alone while leaving the lipid wrapped?
On Tue, Aug 16, 2016 at 12:25 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
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.
On 08/16/2016 11:04 AM, Sachin Natesh wrote:
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!
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