VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed May 15 2019 - 12:12:22 CDT

Right, water molecules diffuse very quickly, so using post-processing steps to unwrap the trajectory have mixed results if your trajectories aren't saved frequently enough (unwrapping only works well if the molecule never moves more than half a periodic box length between frames). My suggestion mostly applied to future simulations, where you would turn off wrapping within the MD engine (wrapAll off in NAMD, for instance).

-Josh

On 2019-05-15 11:09:37-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

When I unwrap the simulation, the micellular molecules stay together. However bizarrely the water molecules immediately start jumping around and move very far away from the reverse micelle its contained in. Why is this and how can I prevent it?

On Mon, May 13, 2019 at 12:26 PM Nick Palmer <tuf90798_at_temple.edu<mailto:tuf90798_at_temple.edu>> wrote:
Hello everyone,
I am simulating two reverse micelles and I need to be able to count the number of water molecules that are in each reverse micelle and out in the solvent for each frame of the simulation. What would be the best way to determine whether or not a water is inside one of these reverse micelles or not? I had tried to find all the waters within a certain amount of distance of the center of mass, but this only works when the two reverse micelles are not next to each other. Also, they don't stay the same shape the whole time so I would have to change the distances at every frame. Is there a way I could use the SASA of the reverse micelle to define a layer, so that I could count the number of water molecules inside and outside of each reverse micelle?
Another issue I have been having is that sometimes the reverse micelles move across periodic boundary conditions, which seems to shift the center of mass for the micelles. How could I use pbc tools to solve this problem since these molecules are not directly attached to each other?
Thank you very much in advance! 

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Nicholas J. Palmer
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Nicholas J. Palmer