[gmx-users] Radius of Gyration

Peter Kroon p.c.kroon at rug.nl
Mon Jul 13 12:02:27 CEST 2015

On 13/07/15 10:40, Daskalakis Vangelis wrote:
> Dear users,
> I am employing gromacs 5.05 to simulate a water cluster (spherical shape)
> forming on some salt in PBC (NVT). I want to calculate the Radius of
> Gyration (Rg, through g_gyrate) throughout the simulation time. I have a
I assume you mean `gmx gyrate`?
> forming water (spherical) cluster, but due to PBC this spherically shaped
> cluster is being constantly partitioned among the edges of a constant
> volume box, resulting in high oscillations for the Rg value. Is there a way
> to put the spherical water cluster in the middle of the constant volume
> box? I have tried trjconv with -center, -fit in all possible options, but
> in vein.
`trjconv -pbc cluster -center ` should do the trick

> P.S. This problem could be reformulated as how I can put a water
> accumulation in the center of the simulation box throughout the simulation
> time, removing any translational motion for a given trajectory. Is it
> possible to have a script processing the trajectory files moving this water
> cluster around the box in order to achieve the minimum Rg value?
> Thank you for your time.
> * <http://www.cut.ac.cy/est/staff/evangelos.daskalakis/>*
> <http://www.cut.ac.cy/>
> <http://www.cut.ac.cy/>

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