[gmx-users] Volume of peripheral protein

Justin Lemkul jalemkul at vt.edu
Thu Mar 15 18:03:26 CET 2018

On 3/14/18 11:02 AM, Pallavi Banerjee wrote:
> Hello gromacs users,
> My system comprises the GFP (protein) anchored to a lipid membrane via a
> polysaccharide. I need to calculate the volume of this peripheral protein
> throughout the simulation. Calculating the volume from the solvent
> accessible surface area is probably not a good idea because the protein
> sleeps on the membrane for a significant part of the trajectory. Could you
> suggest other ways?

The volume computed by gmx sasa is perfectly valid, just don't consider 
the membrane as part of the group for building the surface or for 
output. The shape of the protein is what it is, regardless.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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