[gmx-users] Diffusion of Ammonia Gas

Darrell Koskinen darrellk at ece.ubc.ca
Sun Nov 22 08:59:11 CET 2009

Dear GROMACS-ites,
I am trying to determine whether OPLS can be used to model gas-phase 
ammonia. To this end, I created a 30 nm^3 box with 729 ammonia molecules 
in it, performed energy minimization, and ran a simulation at 298K & 
1.01325 bar for 20 ps followed by another simulation of 20 ps duration 
without temperature or pressure specified. I then ran g_msd on the 
output .trr and .tpr files. The output from g_msd was a diffusion 
constant of:

D[       NH3] 1755.8405 (+/- 1386.3837) 1e-5 cm^2/s

I am first wondering if the simulation length was too short as the error 
seems to be quite large if the figure following the +/- is the error.

Secondly, the value of 1755*1e-5 cm^2 /s is an order of magnitude 
smaller than the value of 0.2*1e-4 m^2 /s, reported in 
/"Landolt-Börnstein IV/15A, Chapter 3: Diffusion in Pure Gases" & 
AMMONIA by Charles E. Baker"/. Therefore, I am also wondering if I am 
performing the simulation correctly and running g_msd correctly.

Please let me know if there is any additional infomation required for 
you to make a determination of whether I am running the simulation 
correctly and thus showing that ammonia as represented in OPLS cannot be 
used for a gas phase simulation or whether I have made a mistake 
somewhere in my runs.

Much thanks.


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