[gmx-users] Radius of Gyration

Daskalakis Vangelis vdas.pilot at gmail.com
Mon Jul 13 10:40:52 CEST 2015

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
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.

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/>*


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