[gmx-users] Does gromacs simulate rotation correctly?

Xavier Periole X.Periole at rug.nl
Fri Oct 24 20:34:55 CEST 2008

On Fri, 24 Oct 2008 10:42:26 -0700
  Arthur Roberts <aroberts99163 at yahoo.com> wrote:
> Hi, all,
> Just curious.  Does gromacs simulate rotation correctly?  From my 
> observation, it would appear that every object in the simulation both  small 
>and large has a similar rotational correlation time, which is  not reality. 
> I would expect water for example to have an extremely  short rotational 
>correlation time with respect to a protein.  I  appreciate your input.
The answer has actually nothing to do with gromacs itself, as it is only
a software. It has to do with the force field used to describe the system.

This said the current force fields describe the rotational diffusion of
water and proteins quite reasonably well. The correlation times are a
bit too small (a factor 2-4) for both water and proteins.
For water (SPC, TIP3P, etc) it would be of the order of picoseconds
For proteins depending (on the size) from one to a few nanoseconds.

So the force fields do reproduce the relative rotational diffusion in
function of the size of the "objects".

> Best wishes,
> Art Roberts
> University of Washington
> Seattle, WA
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XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands

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