[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 31 15:52:31 CET 2011

James Starlight wrote:
> In some papers I found Gromacs graphs showed indirectly measurements of 
> the time evolution of the Area per lipid value. What gromac's program 
> could be used for it for cheacking the above value during simulation runs ?

There is no Gromacs tool for this.  For a simple membrane system, one can use 
g_energy to extract box vectors over time, which can then be divided by the 
number of lipids per leaflet to extract the APL.  For systems with proteins 
embedded in membranes, it is no trivial exercise to make such measurements.  We 
wrote a program several years ago that calculates APL for such systems:


The program can only be run on single snapshots at the moment, but you can 
assemble time evolution from the output.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list