[AMBER] ptraj: msd with diffusion command

From: Bala subramanian <bala.biophysics.gmail.com>
Date: Thu, 23 Aug 2012 16:41:45 +0200

Friends,
I used the diffusion command in ptraj and calculated the msd of just
two water oxygens. The output of the diffusion_a.xmgr is pasted below.

0.000 2.796 1.973 3.426
0.000 5.623 2.482 7.555
0.000 6.151 3.831 7.810
0.000 6.570 3.282 8.693
---- ---- ---- -----
If I understand well, col 2 is the average msd of the two atoms, col 3
is msd of atom1, col 4 is the msd of atom2. I find that the average in
col2 is not equal to what obtain from (col3+col4)/2.
For the first row the average comes as 2.6995. In this case of the
first frame, the difference to what ptraj reports is ~0.09. If we
compare for the second row, it is ~0.6. I see that when I increase the
no of atoms in the calculation, the difference is also increases.

0.000 3.341 1.973 3.209 1.977 3.426 4.593 4.003
0.000 6.135 2.482 3.228 2.227 7.555 8.633 8.523
0.000 6.543 3.831 4.534 2.924 7.810 8.529 8.906
0.000 7.069 3.282 4.525 2.010 8.693 10.177 9.240

Has anyone observed this before ?. Why is it so ?. I am using the
latest ambertools and it was installed after all bug fixes. The
following is the input file I used to run ptraj and the output of the
ptraj is attached.

prnlev 4
trajin PROD.NCDF 1 10
diffusion :3457,3458.O average difdat

Thanks,
Bala

-- 
C. Balasubramanian



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Received on Thu Aug 23 2012 - 08:00:05 PDT
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