On 02/28/12 07:41, surasak chunsrivirot wrote:
>
> Dear all,
>
> I'm wondering if there is a command in AMBER to calculate the volume of a protein from the trajectory. Specifically, I want to calculate the average volume of the protein from the last 10 ns trajectory. Any suggestions on this issue would be greatly appreciated.
Try some of these references as a starting point for some inspiration
about volume measurements using classical MD:
"Molecular dynamics calculation of molecular volumes and volumes of
activation"
http://dx.doi.org/10.1039/c2cp22949h
"Calculation of Molecular Volumes and Volumes of Activation Using
Molecular Dynamics Simulations"
http://dx.doi.org/10.1021/jp209088u
"A combined photothermal and molecular dynamics method for determining
molecular volume changes"
http://dx.doi.org/10.1016/j.cplett.2005.10.093
Regards,
Mark Williamson
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Received on Tue Feb 28 2012 - 07:00:03 PST
