Hi , thanx for your answer . I was running simulations and playing a bit, and I saw that during nve+temp/berendesen temperature was jumping very high from 300K to 3000K etc and I guess thats why I as getting that mistake of : Increase MAXSPECBOND in reaxc.defs.h .
After that I was just running nve , and after a while NVT or nve+temp/berendesen and I was not getting that mistake. I also moticed that NVT was controlling temperature better then nve+temp/berendesen and speed was quite similar .
However , after running system for while in NVE and NVT I have tried to run it in NPT and I have got again same mistake : : Increase MAXSPECBOND in reaxc.defs.h . After that I have used read_restart and I tried to run simulation in NVE and NVT for longer time and then I have switched to NPT , but again I have got same mistake after I have tried with NPT . I dont understand why is this mistake appearing and what should I do to run simulation in NPT , try shorter timestep or what ? (now I use timestep 0.1 and density is arround 0,3 while equilibrated debsity should be arround 0,8) .
Also what I dont understand about fix reax/c species , when I read species file , it is showing me many small fragments and radicals , and not the molecules which I should have in simulation, does it mean that I should average spieces after every 1000 or 10 000 timesteps (instead if every 100) or after equilibration system will “form” molecules which should be there ?
Also what I dont understand about reax is that I need to spend some time in equilibrating system , but reactions can happen during equilibration too , does it mean that I should equilibrate system on lower temperature and then simulate reaction on higher tempeature , or in reax reactions are reversible so after equilibration on same temperature I will get “average” reaction rate ?
I have one more issue with simulation , my solvent is DMSO , but double bond C=S is not parametrized in reax force fields (but people from reax centre have told me to replace it with some another C=S bond from another force field) , but when I try to run simulation I imediately get either mistake : : Increase MAXSPECBOND in reaxc.defs.h or imediately in first timestep that pressure is nan and then I get message “Program.exe has stopped working” and simulation crashes.
If by pair_style reax command I replace S with C I get “acetone” (like alternative solvent) and simulation starts running until NPT (which is the case I already described above) , so any advices why this happens with DMSO ? I guess there is some problem with C=S bond maybe parameters are not good and forces are too big and it says that pressure is nan ?
Any info or explanations or advices would be welcome as I am trying to learn how to run simulations with reax .