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

João Henriques joao.m.a.henriques at gmail.com
Tue Feb 13 20:18:46 CET 2018

You can calculate the asphericity, for example. You just need the
components of the gyration tensor which are given by gmx polystat, if my
memory serves me right.

There are several papers about this. A quick search on Google scholar will
surely produce results.

I would link the papers or the formula, but I'm on the phone. Let me know
if you don't manage to find it yourself.


On Feb 13, 2018 7:52 PM, "Sudip Das" <das.sudip37 at gmail.com> wrote:

> 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
> 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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