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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Dear gromacs users, <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have a protein embedded in a lipid bilayer. After sufficient equilibration of the system ( i.e. size of box X and Box Y became quite constant), I would now like to assess the area per lipid of my system. <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>However, (I think) I could not simply do this ( average size of box X * average size of box Y/ number of lipids per monolayer) because there is a protein in the middle of the bilayer. Ideally I would first like to calculate the area occupied by the protein then take the difference between the two as my answer. I notice this is how the inflategro script calculates the estimated area per lipid during the shrinking process. <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have had a search through the mailing list to look for an answer but to no avail. It seems I might need a script to perform that? <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you for your help.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>HW<o:p></o:p></p></div> <<
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