Mccoyjo at 20:11, 21 June 2005

2005-06-21T20:11:26Z

← Older revision		Revision as of 20:11, 21 June 2005
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	We have access to the param->ir data structure in md.c. If we place a function in the main loop that checks for messages from mother requesting information, we would have all of the following data at our disposal:		We have access to the param->ir data structure in md.c. If we place a function in the main loop that checks for messages from mother requesting information, we would have all of the following data at our disposal:

			from gromacs-3.2.1/include/types/inputrec.h

	typedef struct {		typedef struct {

Mccoyjo at 20:10, 21 June 2005

2005-06-21T20:10:20Z

← Older revision		Revision as of 20:10, 21 June 2005
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			We have access to the param->ir data structure in md.c. If we place a function in the main loop that checks for messages from mother requesting information, we would have all of the following data at our disposal:

	typedef struct {		typedef struct {
	int eI; /* Integration method */		int eI; /* Integration method */

Mccoyjo at 20:07, 21 June 2005

2005-06-21T20:07:43Z

← Older revision		Revision as of 20:07, 21 June 2005
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	int dihre_fc; /* force constant for dihedral restraints */		int dihre_fc; /* force constant for dihedral restraints */
	int nstdihreout; /* frequency of writing dihedrals to enx */		int nstdihreout; /* frequency of writing dihedrals to enx */
	real dr_tau; /* time constant for memory function in disres */		real dr_tau; /* time constant for memory function in disres */
	real orires_fc; /* force constant for orientational restraints */		real orires_fc; /* force constant for orientational restraints */
	real orires_tau; /* time constant for memory function in orires */		real orires_tau; /* time constant for memory function in orires */

Mccoyjo at 20:07, 21 June 2005

2005-06-21T20:07:01Z

New page

typedef struct {
int eI; /* Integration method */
int nsteps; /* number of steps to be taken */
int init_step; /* start at a stepcount >0 (used w. tpbconv) */
int ns_type; /* which ns method should we use? */
int nstlist; /* number of steps before pairlist is generated */
int ndelta; /* number of cells per rlong */
bool bDomDecomp; /* Should we do domain decomposition? */
int decomp_dir; /* Direction of decomposition (may not be opt.) */
int nstcomm; /* number of steps after which center of mass */
/* motion is removed */
int nstcheckpoint; /* checkpointing frequency */
int nstlog; /* number of steps after which print to logfile */
int nstxout; /* number of steps after which X is output */
int nstvout; /* id. for V */
int nstfout; /* id. for F */
int nstenergy; /* number of steps after which energies printed */
int nstxtcout; /* id. for compressed trj (.xtc) */
real init_t; /* initial time (ps) */
real delta_t; /* time step (ps) */
real xtcprec; /* precision of xtc file */
int nkx,nky,nkz; /* number of k vectors in each spatial dimension*/
/* for fourier methods for long range electrost.*/
int pme_order; /* interpolation order for PME */
real ewald_rtol; /* Real space tolerance for Ewald, determines */
/* the real/reciprocal space relative weight */
int ewald_geometry; /* normal/3d ewald, or pseudo-2d LR corrections */
real epsilon_surface; /* Epsilon for PME dipole correction */
bool bOptFFT; /* optimize the fft plan at start */
int ePBC; /* Type of periodic boundary conditions */
bool bUncStart; /* Do not constrain the start configuration */
int etc; /* temperature coupling */
int epc; /* pressure coupling */
int epct; /* pressure coupling type */
real tau_p; /* pressure coupling time (ps) */
tensor ref_p; /* reference pressure (kJ/(mol nm^3)) */
tensor compress; /* compressability ((mol nm^3)/kJ) */
int andersen_seed; /* Random seed for Andersen thermostat. */
real rlist; /* short range pairlist cut-off (nm) */
int coulombtype; /* Type of electrostatics treatment */
real rcoulomb_switch; /* Coulomb switch range start (nm) */
real rcoulomb; /* Coulomb cutoff (nm) */
real epsilon_r; /* relative dielectric constant */
int gb_algorithm; /* Algorithm to use for calculation Born radii */
int nstgbradii; /* Frequency of updating Generalized Born radii */
real rgbradii; /* Cutoff for GB radii calculation */
real gb_saltconc; /* Salt concentration (M) for GBSA models */
int vdwtype; /* Type of Van der Waals treatment */
real rvdw_switch; /* Van der Waals switch range start (nm) */
real rvdw; /* Van der Waals cutoff (nm) */
int implicit_solvent;/* No (=explicit water), or GBSA solvent models */
int eDispCorr; /* Perform Long range dispersion corrections */
real tabext; /* Extension of the table beyond the cut-off, *
* as well as the table length for 1-4 interac. */
real shake_tol; /* tolerance for shake */
real fudgeQQ; /* Id. for 1-4 coulomb interactions */
int efep; /* free energy interpolation no/yes */
real init_lambda; /* initial value for perturbation variable */
real delta_lambda; /* change of lambda per time step (1/dt) */
real sc_alpha; /* free energy soft-core parameter */
real sc_sigma; /* free energy soft-core sigma when c6 or c12=0 */
real dr_fc; /* force constant for ta_disre */
int eDisreWeighting; /* type of weighting of pairs in one restraints */
bool bDisreMixed; /* Use comb of time averaged and instan. viol's */
int nstdisreout; /* frequency of writing pair distances to enx */
real dr_tau; /* time constant for memory function in disres */
real orires_fc; /* force constant for orientational restraints */
real orires_tau; /* time constant for memory function in orires */
int nstorireout; /* frequency of writing tr(SD) to enx */
int dihre_fc; /* force constant for dihedral restraints */
int nstdihreout; /* frequency of writing dihedrals to enx */
real dr_tau; /* time constant for memory function in disres */
real orires_fc; /* force constant for orientational restraints */
real orires_tau; /* time constant for memory function in orires */
int nstorireout; /* frequency of writing tr(SD) to enx */
int dihre_fc; /* force constant for dihedral restraints */
int nstdihreout; /* frequency of writing dihedrals to enx */
real dihre_tau; /* time constant for memory function in dihres */
real em_stepsize; /* The stepsize for updating */
real em_tol; /* The tolerance */
int niter; /* Number of iterations for convergence of */
/* steepest descent in relax_shells */
real fc_stepsize; /* Stepsize for directional minimization */
/* in relax_shells */
int nstcgsteep; /* number of steps after which a steepest */
/* descents step is done while doing cg */
int nbfgscorr; /* Number of corrections to the hessian to keep */
int eConstrAlg; /* Type of constraint algorithm */
int nProjOrder; /* Order of the LINCS Projection Algorithm */
real LincsWarnAngle; /* If bond rotates more than %g degrees, warn */
int nLincsIter; /* Number of iterations in the final Lincs step */
bool bShakeSOR; /* Use successive overrelaxation for shake */
real bd_temp; /* Temperature for Brownian Dynamics (BD) */
real bd_fric; /* Friction coefficient for BD (amu / ps) */
int ld_seed; /* Random seed for SD and BD */
real cos_accel; /* Acceleration for viscosity calculation */
int userint1; /* User determined parameters */
int userint2;
int userint3;
int userint4;
real userreal1;
real userreal2;
real userreal3;
real userreal4;
t_grpopts opts; /* Group options */
t_cosines ex[DIM]; /* Electric field stuff (spatial part) */
t_cosines et[DIM]; /* Electric field stuff (time part) */
} t_inputrec;

Forcing checkpoints in GROMACS - Revision history

Mccoyjo at 20:11, 21 June 2005

Mccoyjo at 20:10, 21 June 2005

Mccoyjo at 20:07, 21 June 2005

Mccoyjo at 20:07, 21 June 2005