[gmx-users] Fast Question on g_msd
ivan.gladich at uochb.cas.cz
Sun Jul 8 18:30:23 CEST 2012
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
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
1 2 3 4 5 11 12 13 14 15 .....
After that, I calculate the diffusivity of all the waters that belong to
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)?
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
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