[gmx-users] Diffusion of Ammonia Gas
David van der Spoel
spoel at xray.bmc.uu.se
Sun Nov 22 10:03:12 CET 2009
Mark Abraham wrote:
> Darrell Koskinen wrote:
>> 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
> I'd guess 20ps is at least one order of magnitude too short. Some
> literature searching might be useful to see how long other people have
> run for making similar observations. A necessary but technically
> insufficient criterion for convergence is that sufficiently long chunks
> of your run agree with themselves, so you may wish to look at the output
> of g_msd on 1ps fragments towards the end of your existing 20ps, or such.
This is an important point, but there is more :). Once you have long
simulation you should check how gaseous your system is, by running
g_clustsize. Ammonia will probably cluster in the gas phase, depending
on temperature of course.
>> 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" &
>> "TEMPERATURE DEPENDENCE OF SELF-DIFFUSION COEFFICIENTS FOR GASEOUS
>> 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.
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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