Both behaviours are possible. Check the -mol option.
Javier
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 (y2.5 and y12.5) -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
-
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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