# nwARGOS example: crown

This example goes through the complete sequence of steps to perform a free energy difference simulation in which Na+ is mutated into K+, complexed to the crown ether 18C6, in aqueous solution.

1. The crown ether wil be built from CH2-O-CH2 fragments. This fragment is not part of the standard segment database. Also a corresponding fragment is not part of the fragment library. The fragment is created using an editor, and should be named coc_______.frg.

2. The fragment just created is force field independent. To create the force field amber dependent segment file, give the command

   `nwsgm coc_______ amber`

   This command searches the fragment libraries and the local file coc_______.frg for a fragment entry `$coc`. The generic atom types defined in the fragment are substituted for the amber atom types. The translation tables are found in the atom type translation library files or the local file coc_______.att, if present. A segment file coc_______.sgm is created that should be renamed to crown.sgm. Alternatively, this file may be appended to amber_u.sgm or amber_r.sgm, provided that these library files are defined in the file $HOME/.nwargos.

3. A sequence file needs to be created, defining the molecular system in terms of segments. Using an editor create the file crown.seq. This file defines the 18C6 crown ether in terms of six cyclicly arranged `coc` fragments. It also specifies the solvent as the SPC/E water model.

4. The topology file crown.top is created, giving the command

   `nwtop crown amber`

   This command searches the amber sequence database files, and the local sequence file crown.seq for a sequence `crown`. The force field needs to be given in order to search the correct database files. If the sequence is found, it searches the amber segment databases and the local segment file crown.sgm for all segments specified in the sequence. When all segments have been found, the topology is generated using the rules appropriate for the force field. All parameters not explicitly given in the segment are added from the amber parameter library files, and the local file crown.par if present. Any segments or parameters not found can be supplied in the local files.