AMBER Archive (2003)

Subject: AMBER: Diffusion constant

From: franck (franck.chevalier_at_iiq.csic.es)
Date: Sat Nov 15 2003 - 13:00:56 CST

Dear amber users.

I am interested in the calculation of the diffusion constant of the molecules of my system and the solvent used is water (TIP3P model at 298 K). For this purpose, I used the diffusion option in ptraj and followed the manual instruction. I got high D values for water (around 4,5) as described in the litterature. This value was obtained without using the image option of ptraj and center the whole system on my solute. But after performing image(center on my solute), I got a D of 2,8 cm2/s closer to the experimental one (2,3 cm2/s at 298 K). Nevertheless, the value is high.

In both case, I first plot the MSD vs time (ps) in a log x log plot to identify the part of the curve to consider (diffusive regime). Then I fitted this curve and got the D value.

I know that the MD I ran were short (2 ns), but I wonder if this high D value could eventually be the result of the diffusion of the water close to the surface of the BOX. More than 2200 water molecules are considered which means that 40 % of the water are in contact with the BOX walls. If one molecule escapes the box from one side and enters again in the box but by the opposite one, the calculated distance could be biased by the dimension of the box ? (a displacement of 2 Angstrom could be interpreted as 2 + the length of the box?).

Thank you,

Chevalier Franck

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