Hello, EMC
I have tried following this topic Polymer with straight backbone - #5 by blue_algae
and I want to make a straight polyethylene chain with using opls-ua force field. My goal is to make crystalline PE structure without using polymer.emc file in the lib folder.
Is there any advice you can offer?
In principal it is not possible to build all-trans chains, even at a temperature of 0 K, due to the fact, that the dihedral function allows for a statistical distribution between cis and trans moieties, with a higher likelihood for trans occurrences. The only way to obtain an all-trans distribution is indeed to use a crystalline input structure. The all-trans distribution of crystalline alkanes is caused by both intra- and intermolecular interactions.
Regarding your confusion: the comments behind the masses in the .data file refer to the types associated with these masses. In the case of OPLS-UA, c2 refers indeed to a CH2 unit, as c32 refers to an methyl CH3 cap group. A short description of types can be found in the Types section under masses in your polymer.emc.gz. Alternatively, you can check the full available set of types in