[AMBER] Very high values of Diffusion coefficient of water

From: DEBOSTUTI GHOSHDASTIDAR <debostutighosh.gmail.com>
Date: Thu, 14 Aug 2014 10:39:52 +0530

Dear Amber Users

I am using AmberTools14's diffusion command to calculate the MSD of bulk
water (TIP3P) for a box of DNA-water simulations. I calculated the MSD for
five 1-ns windows and get an extremely high *D *of ~7x10^-5 cm2/s whereas
the value should be around ~2.3x10^-5 cm2/s. The D of TIP3P is known to be
overestimated but the value I am getting is too high. I use the following

trajin xmd.crd 2001 2500 1

unwrap :1-8046 //all residues
center :1-24 mass origin //DNA residue numbers
image origin center familiar

diffusion 2.0 DNA_water_bulk_win5 :WAT.O average

Thanks in advance for any help

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Received on Wed Aug 13 2014 - 22:30:02 PDT
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