Features

Force Fields

EMC supports force field typing for atomistic force fields.  Force fields can be adapted by the user by altering topology (.top) and parameter (.prm) files, which are found in ./field and subsequent directories.

Available atomistic force fields:

1. -Born for parameters provided by Guillot et al. (Geochim. Cosmochim. Acta 2008, 71, 1249)
   

2. -CHARMM c32b for proteins and lipids
   

3. -CHARMM c36a for proteins, lipids, and water with ions
   

4. -CGENFF as part of CHARMM c36a
   

5. -OPLS-UA as obtained from 2012 files; well-tested
   

6. -OPLS-AA from same files, but not well-tested
   

7. -PCFF with some minor alterations
   

8. -TraPPE as reported in literature, combined with information as found on its website
   

Available coarse-grained force fields:

1. -DPD, but only with standard parameters; parameters can be provided by the user through EMC setup in combination with a parameter file
   

2. -MARTINI, where typing has to be done by the user
   

3. -SDK, also with user typing only
   

 

Type of Builds

EMC allows for an array of builds accessible through the EMC setup script emc_setup.pl, which can be found in ./scripts.  This setup script can be used to either create a build and LAMMPS template for alteration, or serve as part of a simulation workflow.  Created scripts are ready for use with EMC and LAMMPS without the need for alterations.  See the manual under ‘Setup’ for descriptions of some examples.

Options:

1. -Complex mixtures; an unlimited number of molecules can have any desired chemical complexity; quantities are entered in either molecular or mass fractions; see for an example in ./examples/setup/chemistry/bulk
   

2. -Polymers; alternate, block, and random copolymers can be build; the latter can also include complex dendrimers for which each built cluster is different; see for examples in ./examples/setup/chemistry/polymer
   

3. -Surfaces; setup allows for creation of surfaces when a surface definition is available; see for an example in ./examples/setup/chemistry/surface
   

4. -Multiphase systems; this type of setup is used for calculations including interfaces; LAMMPS input scripts always record the pressure tensor, allowing for interfacial tension analysis; optionally, mass profiles can be added; see for an example in ./examples/setup/chemistry/multiphase
   

5. -Simulation environments; loops over multiple simulation conditions can be represented in one setup script, allowing for a clear overview of complex simulations in a succinct manner; see for examples in ./examples/setup/environment/shear and ./examples/setup/environment/shear/t_glass