There is a wonderful tutorial in the Materials Studio help files to calculate the diffusivity of an oxygen atom in PDMS polymer.
I need to modify this to my case where I want to calculate the diffusivity of a small polymer fragment in various solvents. My approach is to first calculate the centroid of the polymer fragment and somehow get the mean square displacement of this centroid (or even better: a set of centroids of the various polymer fragments!)
I can create a centroid, label it, view and modify it's properties; however, I cannot get this centroid to be input in the Discover:Analysis:MSD dialog box.
Can someone help in this regard? I am using the results from an NPT simulation and the frames are visible and an animation can be run.
Alternate approaches are also appreciated. I have also seen forcite but it is not working either.
I need to modify this to my case where I want to calculate the diffusivity of a small polymer fragment in various solvents. My approach is to first calculate the centroid of the polymer fragment and somehow get the mean square displacement of this centroid (or even better: a set of centroids of the various polymer fragments!)
I can create a centroid, label it, view and modify it's properties; however, I cannot get this centroid to be input in the Discover:Analysis:MSD dialog box.
Can someone help in this regard? I am using the results from an NPT simulation and the frames are visible and an animation can be run.
Alternate approaches are also appreciated. I have also seen forcite but it is not working either.
