Dear gromacs users,
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. 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. 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? Thank you for your help. HW << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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