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" &
"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.
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.
[email protected] [email protected] http://folding.bmc.uu.se
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