sander_pmemd_command_line Struct Reference

#include <run_control.h>

List of all members.

Public Attributes
char	AO
	Append/Overwrite files ('A', 'O' or '\0')
char *	mdin
	input control data for the min/md run
char *	mdout
char *	prmtop
	input molecular topology, force field, periodic box type, atom and residue names
char *	inpcrd
	input initial coordinates and (optionally) velocities and periodic box size
char *	restrt
	output final coordinates, velocity, and box dimensions if any - for restarting run
char *	refc
	input (optional) reference coords for position restraints; also used for targeted MD
char *	mdcrd
	output coordinate sets saved over trajectory
char *	inptraj
	input input coordinate sets in trajectory format, when imin=5
char *	mdvel
	output velocity sets saved over trajectory
char *	mden
	output extensive energy data over trajectory
char *	mdinfo
	output latest mdout-format energy info
char *	radii
	Obviously, some sort of radii, but not documented at this point in the manual... (BLF)
char *	inpdip
	input polarizable dipole file, when indmeth=3
char *	rstdip
	output polarizable dipole file, when indmeth=3
char *	cpin
	input protonation state definitions
char *	cprestrt
	protonation state definitions, final protonation states for restart (same format as cpin)
char *	cpout
	output protonation state data saved over trajectory
char *	evbin
	input input for EVB potentials

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Detailed Description

Contains the command-line requirements for a sander/pmemd run.

sander [-help] [-O] [-A] -i mdin -o mdout -p prmtop -c inpcrd -r restrt -ref refc -x mdcrd -y inptraj -v mdvel -e mden -inf mdinfo -radii radii -cpin cpin -cpout cpout -cprestrt cprestrt -evbin evbin

-O Overwrite output files if they exist. -A Append output files if they exist, (used mainly for replica exchange).

Definition at line 71 of file run_control.h.

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Member Data Documentation

char sander_pmemd_command_line::AO

Append/Overwrite files ('A', 'O' or '\0')

Definition at line 72 of file run_control.h.

char* sander_pmemd_command_line::cpin

input protonation state definitions

Definition at line 88 of file run_control.h.

char* sander_pmemd_command_line::cpout

output protonation state data saved over trajectory

Definition at line 90 of file run_control.h.

char* sander_pmemd_command_line::cprestrt

protonation state definitions, final protonation states for restart (same format as cpin)

Definition at line 89 of file run_control.h.

char* sander_pmemd_command_line::evbin

input input for EVB potentials

Definition at line 91 of file run_control.h.

char* sander_pmemd_command_line::inpcrd

input initial coordinates and (optionally) velocities and periodic box size

Definition at line 77 of file run_control.h.

char* sander_pmemd_command_line::inpdip

input polarizable dipole file, when indmeth=3

Definition at line 86 of file run_control.h.

char* sander_pmemd_command_line::inptraj

input input coordinate sets in trajectory format, when imin=5

Definition at line 81 of file run_control.h.

char* sander_pmemd_command_line::mdcrd

output coordinate sets saved over trajectory

Definition at line 80 of file run_control.h.

char* sander_pmemd_command_line::mden

output extensive energy data over trajectory

Definition at line 83 of file run_control.h.

char* sander_pmemd_command_line::mdin

input control data for the min/md run

Definition at line 73 of file run_control.h.

char* sander_pmemd_command_line::mdinfo

output latest mdout-format energy info

Definition at line 84 of file run_control.h.

char* sander_pmemd_command_line::mdout

output user readable state info and diagnostics -o stdout will send output to stdout (to the terminal) instead of to a file.

Definition at line 74 of file run_control.h.

char* sander_pmemd_command_line::mdvel

output velocity sets saved over trajectory

Definition at line 82 of file run_control.h.

char* sander_pmemd_command_line::prmtop

input molecular topology, force field, periodic box type, atom and residue names

Definition at line 76 of file run_control.h.

char* sander_pmemd_command_line::radii

Obviously, some sort of radii, but not documented at this point in the manual... (BLF)

Definition at line 85 of file run_control.h.

char* sander_pmemd_command_line::refc

input (optional) reference coords for position restraints; also used for targeted MD

Definition at line 79 of file run_control.h.

char* sander_pmemd_command_line::restrt

output final coordinates, velocity, and box dimensions if any - for restarting run

Definition at line 78 of file run_control.h.

char* sander_pmemd_command_line::rstdip

output polarizable dipole file, when indmeth=3

Definition at line 87 of file run_control.h.

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The documentation for this struct was generated from the following file:

• inc/AMBER/run_control.h