Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add lammps water example #3

Draft
wants to merge 4 commits into
base: master
Choose a base branch
from
Draft

Add lammps water example #3

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f0afb7f
Initial commit from tip3p water example.
Mar 18, 2020
d7e6690
Add lammps example
rmatsum836 Mar 20, 2020
644f9bf
Fix angle connection_members and clean up input file
rmatsum836 Mar 23, 2020
f53bbee
Add analysis to lammps notebook
rmatsum836 Mar 23, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
33 changes: 33 additions & 0 deletions tip3p-water-box/files/in.tip3p
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
dimension 3
units real
boundary p p p

atom_style full
pair_style lj/cut/coul/long 10
bond_style harmonic
angle_style harmonic
box tilt large
read_data data.tip3p
kspace_style pppm 1.0e-5

velocity all create 300 4928549

fix 1 all shake 1e-6 200 0 b 1 a 1
fix myNVT all nvt temp 300.0 300.0 100.0

neighbor 2.0 bin
neigh_modify delay 0 every 10 check yes

thermo 10
dump nvtdump all atom 100 nvt.lammpstrj
timestep 1
run 5000
log log.equil

undump nvtdump
unfix myNVT

fix myNPT all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 100.0

dump nptdump all atom 100 npt.lammpstrj
run 15000
16 changes: 16 additions & 0 deletions tip3p-water-box/files/tip3p.mol2
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
@<TRIPOS>MOLECULE
RES
3 2 1 0 1
SMALL
NO_CHARGES
@<TRIPOS>CRYSIN
3.0130 3.0130 3.0130 90.0000 90.0000 90.0000 1 1
@<TRIPOS>ATOM
1 O 0.6100 1.0000 1.0000 opls_111 1 opls_111
2 H 0.1700 0.9000 1.7700 opls_112 1 opls_111
3 H 0.1100 1.5400 0.4000 opls_112 1 opls_111
@<TRIPOS>BOND
1 1 2 1
2 3 1 1
@<TRIPOS>SUBSTRUCTURE
1 RES 1 RESIDUE 0 **** ROOT 0
42 changes: 42 additions & 0 deletions tip3p-water-box/files/tip3p.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,42 @@
<?xml version='1.0' encoding='UTF-8'?>
<ForceField name="TIP3P" version="0.0.1">
<FFMetaData>
<Units energy="kJ/mol" mass="amu" charge="elementary_charge" distance="nm"/>
</FFMetaData>
<AtomTypes expression="4*epsilon * ((sigma/r)**12 - (sigma/r)**6)">
<ParametersUnitDef parameter="epsilon" unit="kJ/mol"/>
<ParametersUnitDef parameter="sigma" unit="nm"/>
<AtomType name="opls_111" element="O" charge="-0.834" mass="16" definition="O" description="water O">
<Parameters>
<Parameter name="epsilon" value="0.636386"/>
<Parameter name="sigma" value="0.315061"/>
</Parameters>
</AtomType>
<AtomType name="opls_112" element="H" charge="0.417" mass="1.011" definition="H">
<Parameters>
<Parameter name="epsilon" value="0.0"/>
<Parameter name="sigma" value="1.0"/>
</Parameters>
</AtomType>
</AtomTypes>
<BondTypes expression="0.5 * k * (r-r_eq)**2">
<ParametersUnitDef parameter="k" unit="kJ/mol/nm**2"/>
<ParametersUnitDef parameter="r_eq" unit="nm"/>
<BondType name="BondType-Harmonic-1" type1="opls_111" type2="opls_112">
<Parameters>
<Parameter name="k" value="502416.0"/>
<Parameter name="r_eq" value="0.09572"/>
</Parameters>
</BondType>
</BondTypes>
<AngleTypes expression="0.5 * k * (theta - theta_eq)**2">
<ParametersUnitDef parameter="k" unit="kJ/(mol*radian**2)"/>
<ParametersUnitDef parameter="theta_eq" unit="radian"/>
<AngleType name="AngleType-Harmonic-1" type1="opls_112" type2="opls_111" type3="opls_112">
<Parameters>
<Parameter name="k" value="682.02"/>
<Parameter name="theta_eq" value="1.824218134"/>
</Parameters>
</AngleType>
</AngleTypes>
</ForceField>
Loading