[gmx-users] Radius of Gyration
erik.marklund at chem.ox.ac.uk
Mon Jul 13 14:58:32 CEST 2015
Depending on exactly what you want to measure, gmx clustsize might be useful for you.
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
> On 13 Jul 2015, at 11:48, Daskalakis Vangelis <vdas.pilot at gmail.com> wrote:
> 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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