[gmx-users] Radius of Gyration

[Erik Marklund]

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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