Hi users, using pcff force field I am be able to construct a polymer chain with cation monomer. The SMILES string of the monomer is like this:
And in the last post I uploaded, the missing rules were probably due to the wrong SMILES that I input. There is an imidazole ring on the monomer structure and C-N+ and C-C are not double bonds but partial double bonds, so I just used lower case to represent the ring structure. (sorry for my poor chemistry) I can execute the .esh and build.emc files successfully.
But here comes a problem, how could I insert anions such as Cl- or bistriflimide- NTf2 to make the whole system neutral? My OPTIONS section is like this:
I followed an example polymer.esh in the /v9.4.4/examples/setup/chemistry/polymer/biphase, on which it defined [Na+].[Cl-] salts in GROUPS. So I tried to define pure Cl- anion [Cl-] in my esh GROUPS.
bmim CCCC[n+]1cn(CC)cc1,1, bmim:2
methyl *C,1, bmim:1,1, bmim:2
And in the CLUSTER, I defined their mass portions
And in the POLYMERS, I defined how many monomers should be on a backbone
This esh file can be executed smoothly, but the build.emc file returned an error:
Error: core/system.c:413 SystemChecks:
Total charge of system ‘main’ does not equal zero (charge = -10).
I was confused be cause the mass of 10 monomers + 2 terminators should be 1540, and 10 Cl- anions should be 355, 10 cations and 10 anions yield a neutral system, why the error says the charge of the system is not equal to zero? Did I do something wrong in the GROUPS or CLUSTERS sections?
To those read this post and those who could offer some help, your replies are highly appreciated. Thank you all!!!