[gmx-users] How to calculate the diffusion coefficient in hydration shell?

Hu Zhongqiao zhongqiao_hu at nus.edu.sg
Mon May 22 05:11:49 CEST 2006

Dear all,
I want to to calculate the diffusion coefficient of waters in hydration
shell. I searched the mailing list and found some relevent discussions
about this. But I can't get the clear solution about this yet.
My system includes 8 proteins ( res 1-1216) and H2O (res 1217-5258).
According to the hints in mailing list, I used:
trjorder -f xxx.xtc -s xxx.tpr -n index.ndx -o xxx_ordered.xtc (select
protein as reference group and SOL as molecules group which diffusion
coefficient will be calculated) 
trjconv -f xxx_ordered.xtc -n index.ndx -o xxx.gro
After these, I don't know how to do next in order to get D in hydration
So, could anybody shed any light on my questions as follows:
1, how does trjorder order the SOL molecules? 
I guess that trjorder orders the SOL according to its distance to
protein for every time frame, i.e, the H2O which is the nearest to
protein is labeled the 1st SOL (res no. is 1217, in my case), the H2O
which is the second nearest to protein is labelled the 2nd SOL (res no.
is 1218, in my case), and so on for every time frame. Is it right? That
means from the 1st time frame to 2nd frame, the H2O molecules will be
reordered, right?
2, After using trjorder and trjconv, how to calculate D? I simply used
xxx_ordered.xtc to calculate D of water in hydration shell ( selected
the first 1600 H2O molecules according to the H2O number in the
hydration shell guessed). But I found that the result is too large to be
reasonable. I guess that, from the first frame to second frame, the
molecules with the same labels (r1217, for example) are not the same
molecules because H2O molecules have been reordered. In this case, I can
not figure out how to achieve D.
Any suggesstion are welcome. Thank you very much.
Hu Zhongqiao
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