[gmx-users] Fast Question on g_msd

Javier Cerezo jcb1 at um.es
Mon Jul 9 10:32:06 CEST 2012

Both behaviours are possible. Check the -mol option.


El 08/07/12 18:30, Ivan Gladich escribió:
> Dear all
> I am running a simulation of water slab, i.e. a water system with two 
> air/vacuum interface, using a 5 site water model.
> I am doing a simple test calculating the water diffusivity by mean 
> square displacement in different regions of my water slab.
> In order to do, I created an index that contains all the atoms of the 
> water molecules that belong to a certain region using g_select
> g_select -select " all and same residue as (y>2.5 and y<12.5)" -on 
> select_index.ndx
> At the end, my select_index.ndx contains all the atoms of all the 
> water molecules that are between 2.5 and 12.5 nm
> [all]
> 1 2 3 4 5 11 12 13 14 15 .....
> After that, I calculate the diffusivity of all the waters that belong 
> to this region.
> g_msd -n select_index.ndx -s topol.tpr
> I have a silly question.
> 1) Does g_msd calculate the means square displacement of all the atom 
> that are select_index.ndx (and then it takes the average of all of them)?
> OR
> 2)does g_msd read the topol.tpr, recognize that the atoms in 
> select_index.ndx belong to specific water molecules and so, it 
> calculate the msd based on the displacement of
> the center of mass of each water molecule (and then it takes the 
> average)?
> Sorry, I tried to find something in the archive but I was able (or 
> lucky) to find something.
> Thanks for any possible help
> Ivan
> -----

PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434

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