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doc/src/Section_howto.txt
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@ -184,7 +184,7 @@ commands like "pair_coeff"_pair_coeff.html or
for additional tools that can use CHARMM or AMBER to assign force
field coefficients and convert their output into LAMMPS input.
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force
field. See "(Cornell)"_#Cornell for a description of the AMBER force
field.
@ -439,7 +439,7 @@ computations between frozen atoms by using this command:
6.7 TIP3P water model :link(howto_7),h4
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with
"(MacKerell)"_#howto-MacKerell specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
In LAMMPS the "fix shake"_fix_shake.html command can be used to hold
the two O-H bonds and the H-O-H angle rigid. A bond style of
@ -623,7 +623,7 @@ the partial charge assignemnts change:
O charge = -0.8476
H charge = 0.4238 :all(b),p
See the "(Berendsen)"_#Berendsen reference for more details on both
See the "(Berendsen)"_#howto-Berendsen reference for more details on both
the SPC and SPC/E models.
Wikipedia also has a nice article on "water
@ -2715,7 +2715,7 @@ The thermalized Drude model, similarly to the "core-shell"_#howto_26
model, representes induced dipoles by a pair of charges (the core atom
and the Drude particle) connected by a harmonic spring. The Drude
model has a number of features aimed at its use in molecular systems
("Lamoureux and Roux"_#Lamoureux):
("Lamoureux and Roux"_#howto-Lamoureux):
Thermostating of the additional degrees of freedom associated with the
induced dipoles at very low temperature, in terms of the reduced
@ -2774,7 +2774,7 @@ too close, which can cause numerical issues.
:line
:line
:link(Berendsen)
:link(howto-Berendsen)
[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).
@ -2790,7 +2790,7 @@ J Chem Phys, 120, 9665 (2004).
[(Ikeshoji)] Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261
(1994).
:link(MacKerell)
:link(howto-MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
@ -2812,5 +2812,5 @@ Phys, 79, 926 (1983).
[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
5, 1031-1038 (1993).
:link(Lamoureux)
:link(howto-Lamoureux)
[(Lamoureux and Roux)] G. Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)