[gmx-users] Radius of Gyration

Daskalakis Vangelis vdas.pilot at gmail.com
Mon Jul 13 12:48:02 CEST 2015

Thank you Peter for your reply.

I have tried 'trjconv -pbc cluster -center' before, but despite being
so slow (for around 6000 waters),

I actually get again some spikes on the Rg due to PBC. I will give it
a try again, thank you.

On 13/07/15 12:02, Peter Kroon 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


* <http://www.cut.ac.cy/est/staff/evangelos.daskalakis/>*


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