[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 
>> error.
> 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.

> Mark
>> 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.
>> Darrell

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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