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docs for FEP tip4p type labels

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Jacob Gissinger
2024-08-06 00:04:16 -04:00
parent 1753343727
commit 2627d90adf
1 changed files with 9 additions and 4 deletions
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doc/src/pair_fep_soft.rst
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@ -97,8 +97,8 @@ Syntax
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units)
*lj/cut/tip4p/long/soft* args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2) *lj/cut/tip4p/long/soft* args = otype htype btype atype qdist n alpha_LJ alpha_C cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H otype,htype = atom types (numeric or type label) for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters btype,atype = bond and angle types (numeric or type label) for TIP4P waters
qdist = distance from O atom to massless charge (distance units) qdist = distance from O atom to massless charge (distance units)
n, alpha_LJ, alpha_C = parameters of the soft-core potential n, alpha_LJ, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
@ -125,8 +125,8 @@ Syntax
n, alpha_C = parameters of the soft-core potential n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units) cutoff = global cutoff for Coulomb interactions (distance units)
*tip4p/long/soft* args = otype htype btype atype qdist n alpha_C cutoff *tip4p/long/soft* args = otype htype btype atype qdist n alpha_C cutoff
otype,htype = atom types for TIP4P O and H otype,htype = atom types (numeric or type label) for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters btype,atype = bond and angle types (numeric or type label) for TIP4P waters
qdist = distance from O atom to massless charge (distance units) qdist = distance from O atom to massless charge (distance units)
n, alpha_C = parameters of the soft-core potential n, alpha_C = parameters of the soft-core potential
cutoff = global cutoff for Coulomb interactions (distance units) cutoff = global cutoff for Coulomb interactions (distance units)
@ -161,6 +161,11 @@ Examples
pair_coeff * * 0.155 3.1536 1.0 pair_coeff * * 0.155 3.1536 1.0
pair_coeff 1 1 0.155 3.1536 1.0 9.5 pair_coeff 1 1 0.155 3.1536 1.0 9.5
labelmap atom 1 OW 2 HW
labelmap bond 1 HW-OW
labelmap angle 1 HW-OW-HW
pair_style lj/cut/tip4p/long/soft OW HW HW-OW HW-OW-HW 0.15 2.0 0.5 10.0 9.8
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0
pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
pair_coeff * * 0.28 3.1 1.0 pair_coeff * * 0.28 3.1 1.0