What was the issue you had with g_gyrate? As that is the best tool for this job. Do you have pbc issues?
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of Conrado Pedebos Sent: Friday, 9 September 2011 4:13 AM To: [email protected] Subject: [gmx-users] X and Y dimensions in nanometers Dear gmx-users, I am working with a system composed by 20 molecules which are aggregated in water. I want to calculate the dimensions of this aggregate, but it has an elipsoidal shape, instead of a globular shape, as follows in this representation: | _____|______ -----( ____________)------X | | Y Which gromacs tool could I use to perform this analysis and calculate X and Y (nm) as a function of time? I tried using g_gyrate and observing the Rx, Ry and Rz components, but I couldn't get it right. Thanks in advance, Conrado Pedebos.
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