How does EMC handle polymer Tacticity? I’m trying to find an alternative for using Avogadro to generate monomers for all atom Molecular Dynamics simulations. EMC seems great but the features don’t include any mention of controlling tacticity. For polymers, does EMC assume atacticity? Does it include a parameter to control tacticity?
EMC deals with stereochemistry in the usual way as can be assigned by SMILES (Simplified molecular-input line-entry system - Wikipedia (see Stereochemistry section)). For instance, isotactic polypropylene can be built by
ITEM OPTIONS
replace true
field pcff
number true
temperature 10
focus true
#ntotal 1000
density 0.1
emc_execute true
ITEM END
ITEM GROUPS
monomer *C[C@H](C)*,1,monomer:2
terminator *C,1,monomer:1,1,monomer:2
ITEM END
ITEM CLUSTERS
polymer alternate,1
ITEM END
ITEM POLYMERS
polymer
1 monomer,10,terminator,2
ITEM END
The low temperature is chosen to visually illustrate isotacticity. Please note that stereochemistry works best for linear polymers. Stereochemistry for sugars has issues due to the way EMC builds.
Cis and trans configurations around double bonds are represented in the same manner as in standard SMILES by means of a slash / and backslash \.