VMD-L Mailing List

From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Mon Aug 19 2013 - 16:54:13 CDT

Hi,
I was trying to use "measure gofr" to get a feel for the hydration shells for each residue of the protein in my simulation. However, I'm not very confident in the results and was hoping someone had some experience doing this.

So far I have tried using one atomselection as the alpha carbon of each residue and the other as either "water" or "water and name O". The one complexity I have is that I was using a truncated octahedron created in leap as my unit cell. I wrapped the water using ptraj, but measure gofr says it does not support that geometry for periodic conditions. As a result, I turned it off. I'm not 100% sure how this impacts the calculation.

If anyone has more experience with this, any advice would be appreciated.

Thank you,
Erik

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