[gmx-users] Calculation of shape change of a protein during simulation

Sudip Das das.sudip37 at gmail.com
Tue Feb 13 19:52:02 CET 2018

Dear All,

Is there any way to calculate the change in shape of a protein with respect
to simulation time using GROMACS or VMD? By the use of the word 'shape', I
mean to say 'spherical' or 'elliptical'; or more specifically the value of
eccentricity of the protein wrt simulation time.

My guess is that it can be calculated from the x, y and z components of the
radius of gyration of the protein wrt simulation time. Am I correct?

Thanks in advance.

Best regards,

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India


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