emin

Run simple energy minimization on a frame of a COORDS set.

emin crdset <name> [trajoutname <name>] 
    [rmstol <tol>] 
    [nsteps <#>] 
    [<mask>] 
    [frame <#>] 
    [dx0 <step0>] 
    [out <file>] 
    [{nonbond|openmm}]
    [<potential options>]

crdset <name> COORDS set to use.
[trajoutname <name>] Optional output trajectory for minimization steps.
[rmstol <tol>] Minimum RMS tolerance (default 1E-4).
[nsteps <#>] Number of minimization steps (default 1).
[<mask>] Atoms to minimize (default all).
[frame <#>] Frame from COORDS set to minimize (default 1).
[dx0 <step0>] Size of initial minimization step (default 0.01).
[out <file>] File to write energies to.
[nonbond] If specified, use simple nonbonded potential term in additon to bonded terms.
[openmm] If specified and if CPPTRAJ was compiled with OpenMM support, use OpenMM to calculate the forces. <potential options>
cut <cutoff> Set nonbonded interaction cutoff in Ang. (electrostatics and vdW). Default 8.0.
nexclude <#> Number of bonded atoms within which nonbonded interactions are excluded. Default 4.

THIS COMMAND IS STILL IN DEVELOPMENT AS OF VERSION 5.0.2.

Perform steepest descent minimization on a frame in a COORDS set using a very basic force field (bonds, angles, dihedrals). A simple nonbonded term can be added as well if desired.