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2025-dev-20241008-cf8b9ef
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Gromacs
2025-dev-20241008-cf8b9ef
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#include <gromacs/topology/idef.h>
Union of various interaction paramters.
Some parameters have A and B values for free energy calculations. The B values are not used for regular simulations of course. Free Energy for nonbondeds can be computed by changing the atom type. The harmonic type is used for all harmonic potentials: bonds, angles and improper dihedrals.
No free energy supported for cubic bonds, FENE, WPOL or cross terms.
Public Attributes | |
| struct { | |
| real a | |
| real b | |
| real c | |
| } | bham |
| struct { | |
| real rA | |
| real krA | |
| real rB | |
| real krB | |
| } | harmonic |
| struct { | |
| real klinA | |
| real aA | |
| real klinB | |
| real aB | |
| } | linangle |
| struct { | |
| real lowA | |
| real up1A | |
| real up2A | |
| real kA | |
| real lowB | |
| real up1B | |
| real up2B | |
| real kB | |
| } | restraint |
| struct { | |
| real b0 | |
| real kb | |
| real kcub | |
| } | cubic |
| struct { | |
| real bm | |
| real kb | |
| } | fene |
| struct { | |
| real r1e | |
| real r2e | |
| real krr | |
| } | cross_bb |
| struct { | |
| real r1e | |
| real r2e | |
| real r3e | |
| real krt | |
| } | cross_ba |
| struct { | |
| real thetaA | |
| real kthetaA | |
| real r13A | |
| real kUBA | |
| real thetaB | |
| real kthetaB | |
| real r13B | |
| real kUBB | |
| } | u_b |
| struct { | |
| real theta | |
| real c [5] | |
| } | qangle |
| struct { | |
| real alpha | |
| } | polarize |
| struct { | |
| real alpha | |
| real drcut | |
| real khyp | |
| } | anharm_polarize |
| struct { | |
| real al_x | |
| real al_y | |
| real al_z | |
| real rOH | |
| real rHH | |
| real rOD | |
| } | wpol |
| struct { | |
| real a | |
| real alpha1 | |
| real alpha2 | |
| } | thole |
| struct { | |
| real c6 | |
| real c12 | |
| } | lj |
| struct { | |
| real c6A | |
| real c12A | |
| real c6B | |
| real c12B | |
| } | lj14 |
| struct { | |
| real fqq | |
| real qi | |
| real qj | |
| real c6 | |
| real c12 | |
| } | ljc14 |
| struct { | |
| real qi | |
| real qj | |
| real c6 | |
| real c12 | |
| } | ljcnb |
| struct { | |
| real phiA | |
| real cpA | |
| int mult | |
| real phiB | |
| real cpB | |
| } | pdihs |
| Proper dihedrals. More... | |
| struct { | |
| real dA | |
| real dB | |
| } | constr |
| struct { | |
| real doh | |
| real dhh | |
| } | settle |
| SETTLE. More... | |
| struct { | |
| real b0A | |
| real cbA | |
| real betaA | |
| real b0B | |
| real cbB | |
| real betaB | |
| } | morse |
| struct { | |
| real pos0A [DIM] | |
| real fcA [DIM] | |
| real pos0B [DIM] | |
| real fcB [DIM] | |
| } | posres |
| struct { | |
| real pos0 [DIM] | |
| real r | |
| real k | |
| int geom | |
| } | fbposres |
| struct { | |
| real rbcA [NR_RBDIHS] | |
| real rbcB [NR_RBDIHS] | |
| } | rbdihs |
| struct { | |
| real cbtcA [NR_CBTDIHS] | |
| real cbtcB [NR_CBTDIHS] | |
| } | cbtdihs |
| struct { | |
| real a | |
| real b | |
| real c | |
| real d | |
| real e | |
| real f | |
| } | vsite |
| struct { | |
| int n | |
| real a | |
| } | vsiten |
| struct { | |
| real low | |
| real up1 | |
| real up2 | |
| real kfac | |
| int type | |
| int label | |
| int npair | |
| } | disres |
| struct { | |
| real phiA | |
| real dphiA | |
| real kfacA | |
| real phiB | |
| real dphiB | |
| real kfacB | |
| } | dihres |
| struct { | |
| int ex | |
| int power | |
| int label | |
| real c | |
| real obs | |
| real kfac | |
| } | orires |
| struct { | |
| int table | |
| real kA | |
| real kB | |
| } | tab |
| struct { | |
| int cmapA | |
| int cmapB | |
| } | cmap |
| struct { | |
| real buf [MAXFORCEPARAM] | |
| } | generic |
| struct { ... } t_iparams::pdihs |
Proper dihedrals.
Proper dihedrals can not have different multiplicity when doing free energy calculations, because the potential would not be periodic anymore.
| struct { ... } t_iparams::settle |
SETTLE.
SETTLE can not be used for Free energy calculations of water bond geometry. Use shake (or lincs) instead if you have to change the water bonds.
1.8.5