[gmx-users] Radius of Gyration

[Daskalakis Vangelis]

Thank you Erik for your answer. That might be helpful as well, I will give
it a try to have an estimation of the cluster size.


On Mon, Jul 13, 2015 at 3:58 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk>
wrote:

> Depending on exactly what you want to measure, gmx clustsize might be
> useful for you.
>
> Erik
>
>
> Erik Marklund, PhD
> Postdoctoral Research Fellow
> Fulford JRF, Somerville College
>
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>
> > 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
> >
> > Peter
> >
> >
> > * <http://www.cut.ac.cy/est/staff/evangelos.daskalakis/>*
> > <http://www.cut.ac.cy/>
> >
> > <http://www.cut.ac.cy/>
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