[gmx-users] g-msd diffusion of molecules
Jun Soo Kim
jskim9 at wisc.edu
Thu Jan 18 17:14:00 CET 2007
I am trying to calculate the self diffusion coefficient of water
molecules with tip5p water model.
Based on the manual, it seems that there can be two ways to calculate
the diffusion of water molecules, not atoms :
1. Select the group of ( OW, HW1, HW2 ) of tip5p water in index.ndx
to calculate the MSD. Because -mw is set as 'yes' by default, the MSD
calculated is for the center of mass of tip5p water molecules.
2. Select the group of molecule numbers in index.ndx to calculate the
MSD. This time, use option -mol to calculate the MSD of molecules.
Could anyone tell me if they are ok and, if so, which one is more
And the method 2 above seems to be reasonable, but I am afraid that
the mass of virtual sites OL1 and OL2 may also be counted when it
calculate the center-of-mass MSD. Actually, this problem happens when
we use genbox to generate the water box with tip5p. The density of
water box is way too low for tip5p when it is generated by genbox
because genbox counts the masses of OL1 and OL2 when it calculates
the density. Is it still safe to use the method 2 to calculate the
MSD for tip5p water model?
Thanks in advance.
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