ReaDDy fusion reaction error
Posted: Thu May 14, 2015 6:29 pm
Hello,
I am trying to set up the following fusion reaction:
A + B <–> C (k_on = 50000 k_off = 5).
This is the code I am using:
However I get the following error:
I am trying to set up the following fusion reaction:
A + B <–> C (k_on = 50000 k_off = 5).
This is the code I am using:
Code: Select all
<reaction>
<name>rxn1_fusion</name>
<type>fusion</type>
<educts>
<educt type="particle">A</educt>
<educt type="particle">B</educt>
</educts>
<products>
<product type="particle">C</product>
</products>
<k_forward>50000</k_forward>
<k_backward>5</k_backward>
</reaction>
why do you think this is happening?top: 'step 3000'
analysis...
3000 -> analysis by 0_standard_traj|tplgyCoords -> out_traj.xml ...
3000 -> analysis by 1_vmdReadable_traj_tutorial|xyz -> out_traj_vmdCapable.xyz ...
3000 -> analysis by 2_msd_gnuplot|csv -> out_msd.csv ...
MSD(XYZ) typeId:0: 277.03094997931294 nParticles 980
MSD(XYZ) typeId:1: 243.37722919390936 nParticles 25
MSD(XYZ) typeId:2: 1201.8071470152047 nParticles 3
3000 -> analysis by 3_rdf_gnuplot|csv -> out_rdf.csv ...
RdfComputer.setup(): sphericalSurface=false
r[nm]:200.0 maxDistanceOnSphere[nm]: 400.0 nBins: 1000 binWidth[nm]: 0.4
check From 0
check to 0
3000 -> analysis by 4_particleNumbers|csv -> out_particleNumbers.csv ...
3000 -> analysis by 5_standardReactionReporting|csv -> out_reactions.csv ...
reset flag enabled.
Exception in thread "main" java.lang.RuntimeException: requested particle ID '17'is unknown
at readdy.impl.sim.core.config.ParticleConfiguration.getParticle(ParticleConfiguration.java:211)
at readdy.impl.sim.core.Core.step(Core.java:154)
at readdy.impl.sim.top.Top.runSimulation(Top.java:117)
at readdy.impl.sim.ReaDDySimulator.runSimulation(ReaDDySimulator.java:51)
at readdy.Main.main(Main.java:120)
done