Calculate energies using via SANDER; requires compilation with the SANDER API.
esander [<name>] [out <filename>] [saveforces] [parmname <file>] [keepfiles] [<namelist vars> ...]
[<name>] Data set name.
[out <filename>] File to write results to.
[saveforces] If specified, save forces to frames. Requires writing frames in NetCDF format.
[parmname <file>] Name of temporary topology file (default: ’CpptrajEsander.parm7’).
[keepfiles] Keep temporary topology file after program execution.
[<namelist vars>] Namelist variables supported by the sander API in format ’var <value>’; see below.
Calculate energies for input frames using the sander API. It requires compilation with the SANDER API (sanderlib). This can be considered as a faster alternative to energy post-processing with sander (imin = 5). Currently the following sander namelist variables are supported: extidel, intdiel, rgbmax, saltcon, cut, dielc, igb, alpb, gbsa,
lj1264, ipb, inp, vdwmeth, ew_type, ntb, ntf, ntc. See the SANDER entry of the AMBER manual for details. If ntb/cut/igb are not specified CPPTRAJ will attempt to pick reasonable values based on the input system. The defaults for a non-periodic system are ntb=0, cut=9999.0, igb=1. The defaults for a periodic system are ntb=1, cut=8.0, igb=0. This currently requires writing a temporary Amber topology, the name of which can be set by
keepfiles is specified this temporary topology will not be deleted after execution.
For example, to calculate energies for a non-periodic system using igb=1 (the default) with GB surface area turned on (gbsa=1):
parm DPDP.parm7 trajin DPDP.nc esander DPDP out Edpdp.dat gbsa 1