+Syntax: +
+pair_style style distance_cutoff angle_cutof N ++
Examples: +
+pair_style hbond/dreiding/lj 4 5.0 90 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 2 ++
pair_style hbond/dreiding/morse 2 4.6 75.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 4 3.0 ++
Description: +
+The hbond/dreiding styles compute the Acceptor-Hydrogen-Donor (AHD) +3-body hydrogen bond interaction for the +DREIDING force field, given by: +
+
+where Rc is the distance cutoff, theta_c is the angle cutoff, and n is +the cosine periodicity. +
+Here, r is the radial distance between the donor (D) and acceptor +(A) atoms and theta is the bond angle between the acceptor, the +hydrogen (H) and the donor atoms: +
+
+These 3-body interactions can be defined for pairs of acceptor and +donor atoms, based on atom types. For each donor/acceptor atom pair, +the 3rd atom in the interaction is a hydrogen permanently bonded to +the donor atom, e.g. in a bond list read in from a data file via the +read_data command. The atom types of possible +hydrogen atoms for each donor/acceptor type pair are specified by the +pair_coeff command (see below). +
+Style hbond/dreiding/lj is the original DREIDING potential of +(Mayo). It uses a LJ 12/10 functional for the Donor-Acceptor +interactions. To match the results in the original paper, use n = 4. +
+Style hbond/dreiding/morse is an improved version using a Morse +potential for the Donor-Acceptor interactions. (Liu) showed +that the Morse form gives improved results for Dendrimer simulations, +when n = 2. +
+See this howto section of the manual for more +information on the DREIDING forcefield. +
+Because the Dreiding hydrogen bond potential is only one portion of +an overall force field which typically includes other pairwise +interactions, it is common to use it as a sub-style in a pair_style +hybrid or hybrid/overlay command. +
+The following coefficients must be defined for pairs of eligible +donor/acceptor types via the pair_coeff command as +in the examples above. +
+IMPORTANT NOTE: Unlike other pair styles and their associated +pair_coeff commands, you do not need to specify +pair_coeff settings for all possible I,J type pairs. Only I,J type +pairs for atoms which act as joint donors/acceptors need to be +specified; all other type pairs are assumed to be inactive. +
+IMPORTANT NOTE: A pair_coeff command can be +speficied multiple times for the same donor/acceptor type pair. This +enables multiple hydrogen types to be assigned to the same +donor/acceptor type pair. For other pair_styles, if the pair_coeff +command is re-used for the same I.J type pair, the settings for that +type pair are overwritten. For the hydrogen bond potentials this is +not the case; the settings are cummulative. This means the only way +to turn off a previous setting, is to re-use the pair_style command +and start over. +
+For the hbond/dreiding/lj style the list of coefficients is as +follows: +
+For the hbond/dreiding/morse style the list of coefficients is as +follows: +
+A single hydrogen atom type K can be specified, or a wild-card +asterisk can be used in place of or in conjunction with the K +arguments to select multiple types as hydrogens. This takes the form +"*" or "*n" or "n*" or "m*n". See the pair_coeff command +doc page for details. +
+If the donor flag is i, then the atom of type I in the pair_coeff +command is treated as the donor, and J is the acceptor. If the donor +flag is j, then the atom of type J in the pair_coeff command is +treated as the donor and I is the donor. This option is required +because the pair_coeff command requires that I <= J. +
+Epsilon and sigma are settings for the hydrogen bond potential based +on a Lennard-Jones functional form. Note that sigma is defined as the +zero-crossing distance for the potential, not as the energy minimum at +2^(1/6) sigma. +
+D0 and alpha and r0 are settings for the hydrogen bond potential based +on a Morse functional form. +
+The last 3 coefficients for both styles are optional. If not +specified, the global n, distance cutoff, and angle cutoff specified +in the pair_style command are used. If you wish to only override the +2nd or 3rd optional parameter, you must also specify the preceding +optional parameters. +
+Mixing, shift, table, tail correction, restart, rRESPA info: +
+These pair styles do not support mixing. You must explicitly identify +each donor/acceptor type pair. +
+These styles do not support the pair_modify shift +option for the energy of the interactions. +
+The pair_modify table option is not relevant for +these pair styles. +
+These pair styles do not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +
+These pair styles do not write their information to binary restart +files, so pair_style and pair_coeff commands need to be +re-specified in an input script that reads a restart file. +
+These pair styles can only be used via the pair keyword of the +run_style respa command. They do not support the +inner, middle, outer keywords. +
+These pair style tally a count of how many hydrogen bonding +interactions they calculate each timestep. This quantity can be +accessed via the compute pair command as a vector +of values of length 1. +
+To print this quantity to the log file (with a descriptive column +heading) the following commands could be included in an input script: +
+compute hb all pair hbond/dreiding/lj +variable hb equal c_hb[1] +thermo_style custom step temp epair v_hb ++
Restrictions: none +
+Related commands: +
+ +Default: none +
+(Mayo) Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). +
+ + +(Liu) Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) +2798 (2009) +
+ diff --git a/doc/pair_hbond_dreiding.txt b/doc/pair_hbond_dreiding.txt new file mode 100644 index 0000000000..d309d43908 --- /dev/null +++ b/doc/pair_hbond_dreiding.txt @@ -0,0 +1,198 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style hbond/dreiding/lj command :h3 +pair_style hbond/dreiding/morse command :h3 + +[Syntax:] + +pair_style style distance_cutoff angle_cutof N :pre + +style = {hbond/dreiding/lj} or {hbond/dreiding/morse} +n = cosine angle periodicity +distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units) +angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor +interactions (degrees) :ul + +[Examples:] + +pair_style hbond/dreiding/lj 4 5.0 90 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 2 :pre + +pair_style hbond/dreiding/morse 2 4.6 75.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 4 3.0 :pre + +[Description:] + +The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD) +3-body hydrogen bond interaction for the +"DREIDING"_Section_howto.html#4_4 force field, given by: + +:c,image(Eqs/pair_hbond_dreiding.jpg) + +where Rc is the distance cutoff, theta_c is the angle cutoff, and n is +the cosine periodicity. + +Here, {r} is the radial distance between the donor (D) and acceptor +(A) atoms and {theta} is the bond angle between the acceptor, the +hydrogen (H) and the donor atoms: + +:c,image(Eqs/dreiding_hbond.jpg) + +These 3-body interactions can be defined for pairs of acceptor and +donor atoms, based on atom types. For each donor/acceptor atom pair, +the 3rd atom in the interaction is a hydrogen permanently bonded to +the donor atom, e.g. in a bond list read in from a data file via the +"read_data"_read_data.html command. The atom types of possible +hydrogen atoms for each donor/acceptor type pair are specified by the +"pair_coeff"_pair_coeff.html command (see below). + +Style {hbond/dreiding/lj} is the original DREIDING potential of +"(Mayo)"_#Mayo. It uses a LJ 12/10 functional for the Donor-Acceptor +interactions. To match the results in the original paper, use n = 4. + +Style {hbond/dreiding/morse} is an improved version using a Morse +potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed +that the Morse form gives improved results for Dendrimer simulations, +when n = 2. + +See this "howto section"_Section_howto.html#4_4 of the manual for more +information on the DREIDING forcefield. + +Because the Dreiding hydrogen bond potential is only one portion of +an overall force field which typically includes other pairwise +interactions, it is common to use it as a sub-style in a "pair_style +hybrid or hybrid/overlay"_pair_hybrid.html command. + +The following coefficients must be defined for pairs of eligible +donor/acceptor types via the "pair_coeff"_pair_coeff.html command as +in the examples above. + +IMPORTANT NOTE: Unlike other pair styles and their associated +"pair_coeff"_pair_coeff.html commands, you do not need to specify +pair_coeff settings for all possible I,J type pairs. Only I,J type +pairs for atoms which act as joint donors/acceptors need to be +specified; all other type pairs are assumed to be inactive. + +IMPORTANT NOTE: A "pair_coeff"_pair_coeff.html command can be +speficied multiple times for the same donor/acceptor type pair. This +enables multiple hydrogen types to be assigned to the same +donor/acceptor type pair. For other pair_styles, if the pair_coeff +command is re-used for the same I.J type pair, the settings for that +type pair are overwritten. For the hydrogen bond potentials this is +not the case; the settings are cummulative. This means the only way +to turn off a previous setting, is to re-use the pair_style command +and start over. + +For the {hbond/dreiding/lj} style the list of coefficients is as +follows: + +K = hydrogen atom type = 1 to Ntypes +donor flag = {i} or {j} +epsilon (energy units) +sigma (distance units) +n = exponent in formula above +distance cutoff (distance units) +angle cutoff (degrees) :ul + +For the {hbond/dreiding/morse} style the list of coefficients is as +follows: + +K = hydrogen atom type = 1 to Ntypes +donor flag = {i} or {j} +D0 (energy units) +alpha (1/distance units) +r0 (distance units) +n = exponent in formula above +distance cutoff (distance units) +angle cutoff (degrees) :ul + +A single hydrogen atom type K can be specified, or a wild-card +asterisk can be used in place of or in conjunction with the K +arguments to select multiple types as hydrogens. This takes the form +"*" or "*n" or "n*" or "m*n". See the "pair_coeff"_pair_coeff command +doc page for details. + +If the donor flag is {i}, then the atom of type I in the pair_coeff +command is treated as the donor, and J is the acceptor. If the donor +flag is {j}, then the atom of type J in the pair_coeff command is +treated as the donor and I is the donor. This option is required +because the "pair_coeff"_pair_coeff.html command requires that I <= J. + +Epsilon and sigma are settings for the hydrogen bond potential based +on a Lennard-Jones functional form. Note that sigma is defined as the +zero-crossing distance for the potential, not as the energy minimum at +2^(1/6) sigma. + +D0 and alpha and r0 are settings for the hydrogen bond potential based +on a Morse functional form. + +The last 3 coefficients for both styles are optional. If not +specified, the global n, distance cutoff, and angle cutoff specified +in the pair_style command are used. If you wish to only override the +2nd or 3rd optional parameter, you must also specify the preceding +optional parameters. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +These pair styles do not support mixing. You must explicitly identify +each donor/acceptor type pair. + +These styles do not support the "pair_modify"_pair_modify.html shift +option for the energy of the interactions. + +The "pair_modify"_pair_modify.html table option is not relevant for +these pair styles. + +These pair styles do not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +These pair styles do not write their information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands need to be +re-specified in an input script that reads a restart file. + +These pair styles can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. They do not support the +{inner}, {middle}, {outer} keywords. + +These pair style tally a count of how many hydrogen bonding +interactions they calculate each timestep. This quantity can be +accessed via the "compute pair"_compute_pair.html command as a vector +of values of length 1. + +To print this quantity to the log file (with a descriptive column +heading) the following commands could be included in an input script: + +compute hb all pair hbond/dreiding/lj +variable hb equal c_hb\[1\] +thermo_style custom step temp epair v_hb :pre + +:line + +[Restrictions:] none + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Mayo) +[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 +(1990). + +:link(Liu) +[(Liu)] Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) +2798 (2009)