How to do something¶
This page shows you how to use DL_FIELD to acheive a specific task.
Content
How to setup a liquid model
How to setup a solution model
Setup constrained bond model
Using xyz input files
How to setup a multiple potential model
How to set up a liquid model
- Create a single-molecule configuration file. This would be the liquid molecule, or the solute molecule if you were to setup a solution. Let’s call this file molecule.xyz
- Edit your DL_FIELD control file as follows:
Example file of setting up liquid
1 * Construct DL_POLY output files
0 * Unuse slot.
opls2005 * Type of force field require (see list below for choices).
kcal/mol * Energy unit: kcal/mol, kJ/mol, eV, or K.
normal * Conversion criteria (strict, normal, loose)
1 * Bond type (0=default, 1=harmonic , 2=Morse)
1 * Angle type (0=default, 1=harmonic, 2=harmonic cos)
none * Include user-defined information. Put 'none' or a .udff filename
1 * Verbosity mode: 1 = on, 0 = off
molecule.xyz * Configuration file.
none * Output file in PDB. Put 'none' if not needed.
1 1.05 g/cm^3 1.6 * Solution Maker: on/off, density, unit, cutoff)
1 * Optimise FIELD output size, if possible? 1=yes 0=no
2 * Atom display: 1 = DL_FIELD format. 2 = Standard format
2 * Vdw display format: 1 = 12-6 format 2 = LJ format
default * Epsilon mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic
default * Sigma mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic
1 * Epsilon mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
2 * Sigma mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
1 * Epsilon mixing rule (BETWEEN different FF) : 1 = geometric 2 = arithmatic
1 * Sigma mixing rule (BETWEEN different FF): 1 = geometric 2 = arithmatic
0 * Display additional info. for protein 1=Yes 0=No
0 * Freeze atoms? 1 = Yes (see below) 0 = No
0 * Tether atoms? 1 = Yes (see below) 0 = No
0 * Constrain bonds? 1 = Yes (see below) 0 = No
0 * Apply rigid body? 1 = Yes (see below) 0 = No
1 * Periodic condition ? 0=no, other number = type of box (see below)
40.0 0.0 0.0 * Cell vector a (x, y, z)
0.0 40.0 0.0 * Cell vector b (x, y, z)
0.0 0.0 40.0 * Cell vector c (x, y, z)
default * 1-4 scaling for coulombic (put default or x for scaling=x)
default * 1-4 scaling for vdw (put default or x for scaling=x)
0 300.0 * Include velocity? 1=yes, 0=no and scaling temperature.
1 * Position solute at origin? 1 = yes, 0=no
none 2.0 default * Solvate model? none or specify solvent (see below) and distance criteria.
0 10.0 * Add counter ions? 1=yes, 0=no, minimum distance from solute
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The example shows OPLS2005 FF scheme is used. The Solution Maker feature is also turn on:
1 1.05 g/cm^3 1.6
This means: ‘Switch on (1) the feature, duplicate structure in the molecule.xyz file, to create a density of 1.05 g/cm^3, with each molecule at least 1.6 angstrom apart.
The number of molecules duplicated will depend on the cell vectors defined, which is 40 angstrom in x,y and z directions.
- Run DL_FIELD
Tip
Once the system is setup, it is recommended to view your dl_poly.CONFIG structure in a graphical display software to make sure the structure is evenly distributed. You can adjust the distance accordingly and rerun DL_FIELD. A smaller distance means molecules will be tightly packed against each other. Whereas, large distance means the molecules are more widely apart.
How to setup a solution model
Use the same procedures for setting up liquid as described above. However, use the Solvation feature in the DL_FIELD control file as shown below:
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none * Include user-defined information. Put 'none' or a .udff filename
1 * Verbosity mode: 1 = on, 0 = off
molecule.xyz * Configuration file.
none * Output file in PDB. Put 'none' if not needed.
1 1.5 mol/dm^3 4.0 * Solution Maker: on/off, density, unit, cutoff)
1 * Optimise FIELD output size, if possible? 1=yes 0=no
2 * Atom display: 1 = DL_FIELD format. 2 = Standard format
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0 * Apply rigid body? 1 = Yes (see below) 0 = No
1 * Periodic condition ? 0=no, other number = type of box (see below)
40.0 0.0 0.0 * Cell vector a (x, y, z)
0.0 40.0 0.0 * Cell vector b (x, y, z)
0.0 0.0 40.0 * Cell vector c (x, y, z)
default * 1-4 scaling for coulombic (put default or x for scaling=x)
default * 1-4 scaling for vdw (put default or x for scaling=x)
0 300.0 * Include velocity? 1=yes, 0=no and scaling temperature.
1 * Position solute at origin? 1 = yes, 0=no
tip4p 2.0 default * Solvate model? none or specify solvent (see below) and distance criteria.
0 10.0 * Add counter ions? 1=yes, 0=no, minimum distance from solute
0 * MM energy calculation. 1=Yes, 0=No
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In this example, the Solution Maker feature will, firstly, duplicate your solute molecules in the simulation box to give a concentration of 1.5 mol/dm^3 and each molecule is at least 4 angstrom apart. Secondly, the simulation box is solvated with the TIP4P water model. The solvent molecules must not be located less than 2.0 angstrom from the solute molecules.
Note
You can only solvate your system if it is a cubic or orthorhombic.
Of course, you can also solvate your system with other types of solvent. There is a (growing) list of solvent you can choose, which is found in the file call solvent_list in the solvent/ directory.
Warning
Depending on the FF schemes, you may get an error in DL_FIELD if there is no MOLECULE template or potential parameters available for some solvent molecules. In addition, you cannot solvate your system if an inorganic FF scheme is used.
How to setup a constraint bond model
Constraining bonds are one of the effective way to remove fastest mode of motion in your system, that is, the bond vibration, especially bonds that contain the hydrogen atoms.
- Provide a Molecular Group name to your molecules, if you are using xyz of PDB file. If you don’t know how to do that, consult this page. If you don’t do that, DL_FIELD will assign a default name called not_define.
- Edit your DL_FIELD control file.
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1 * Optimise FIELD output size, if possible? 1=yes 0=no
2 * Atom display: 1 = DL_FIELD format. 2 = Standard format
2 * Vdw display format: 1 = 12-6 format 2 = LJ format
default * Epsilon mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic
default * Sigma mixing rule (organic FF only) : default, or 1 = geometric, 2 = arithmatic
1 * Epsilon mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
2 * Sigma mixing rule (inorganic FF only) : 1 = geometric 2 = arithmatic
1 * Epsilon mixing rule (BETWEEN different FF) : 1 = geometric 2 = arithmatic
1 * Sigma mixing rule (BETWEEN different FF): 1 = geometric 2 = arithmatic
0 * Display additional info. for protein 1=Yes 0=No
0 * Freeze atoms? 1 = Yes (see below) 0 = No
0 * Tether atoms? 1 = Yes (see below) 0 = No
1 * Constrain bonds? 1 = Yes (see below) 0 = No
0 * Apply rigid body? 1 = Yes (see below) 0 = No
1 * Periodic condition ? 0=no, other number = type of box (see below)
40.0 0.0 0.0 * Cell vector a (x, y, z)
0.0 40.0 0.0 * Cell vector b (x, y, z)
0.0 0.0 40.0 * Cell vector c (x, y, z)
default * 1-4 scaling for coulombic (put default or x for scaling=x)
default * 1-4 scaling for vdw (put default or x for scaling=x)
0 300.0 * Include velocity? 1=yes, 0=no and scaling temperature.
1 * Position solute at origin? 1 = yes, 0=no
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########################################################
Atom state specification: type Molecular_Group filter [value]
FREEZE A
RIGID A
CONSTRAIN ORG1 h-bond
CONSTRAIN ORG2 all
#########################################################
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Switch on (1) the Constrain bonds. It instructs DL_FIELD to look for which group of molecules to apply the constrain according to the CONSTRAIN directive statements shown below. If this is turn off (0), no constrain bond will be setup.
At the Atom state specification section, define how the bonds would be constrained. In this example, it shows two statements:
CONSTRAIN ORG1 h-bond
CONSTRAIN ORG2 all
These directive statements instruct DL_FIELD to constrain only bonds that contain hydrogen atoms on molecules belong to the Molecular Group ORG1. Whereas, all bonds will be constrained for molecules belong to Molecular Group ORG2.
- Run DL_FIELD
Note
Only one type of bond constrain can be applied in each Molecular Group.
Warning
If the Molecular Group names in the configuration file do not match with any of the CONSTRAIN directive statements, no bond constrain will be applied. DL_FIELD does not consider this as an error.
How to use xyz file structure
The xyz file format is the simplest format one could use in DL_FIELD to setup force field models. In general, atoms must be expressed in standard element symbols together with the corresponding xyz coordinates.
For organic systems, this is a must. DL_FIELD will attempt to determine the ATOM_KEYs depending on the FF scheme chosen. For inorganic systems, you can use either the element symbols or ATOM_KEYs. Below show a few examples for different types of systems.
- A typical organic system, with optional directives CRYST1, which defines the simulation box size, and MOLECULAR_GROUP directive, which gives a name to a group of atoms and molecules.
5303
CRYST1 30.000 40.000 30.000 90.00 90.00 90.00
# MOLECULAR_GROUP solute
C -1.175000 1.554000 0.000000
O -1.171000 2.697000 -0.443000
C -2.448000 0.747000 0.204000
O -0.068000 0.852000 0.366000
H -2.431000 -0.161000 -0.399000
H -2.573000 0.480000 1.253000
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# MOLECULAR_GROUP solvent
O -3.337848 -2.911992 8.337031
H -3.219666 -2.418653 7.475260
H -3.864043 -2.348754 8.974120
O -0.864896 -1.797776 3.460864
H -0.308157 -2.150110 2.708599
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- For inorganic systems, the additional directive MOLECULE_KEY must always be specified. Example below shows a small sample of illite clay, expressed in element symbols. The MOLECULE_KEY CLYF indicate the structure can be matched with the MOLECULE general_CLAYFF template. To set up the force field, the inorganic_clay FF scheme must be used in the DL_FIELD control file.
984
CRYST1 20.9320 27.1146 37.9124 90.00 90.00 90.00
# MOLECULAR_GROUP clay MOLECULE_KEY CLYF
Al 2.502740 2.481160 3.429950
Al 2.449260 8.524460 3.476860
Al 3.428830 3.929990 0.755898
Al -0.143951 3.969300 3.422410
Al -0.173622 6.953530 3.466610
Si 1.473570 3.925650 6.223150
Si 1.450440 7.013190 6.226930
Si 4.066990 8.448000 6.234750
Si 4.095880 2.490110 6.237170
Si 3.324740 7.046450 0.839732
Si 0.717297 8.490300 0.870192
Si 0.830225 2.515690 0.793637
O 1.463210 3.781760 4.625190
O 2.764240 3.176920 6.929140
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Alternatively, the atoms can be expressed in ATOM_KEYs. Example below shows the same illite clay sample. DL_FIELD has better chances to setup the FF model successfully, but this requires the user to pre-assign the correct ATOM_KEYs to the file.
984
CRYST1 20.9320 27.1146 37.9124 90.00 90.00 90.00
# MOLECULAR_GROUP clay MOLECULE_KEY CLYF
ao 2.502740 2.481160 3.429950
ao 2.449260 8.524460 3.476860
ao 3.428830 3.929990 0.755898
ao -0.143951 3.969300 3.422410
ao -0.173622 6.953530 3.466610
st 1.473570 3.925650 6.223150
st 1.450440 7.013190 6.226930
st 4.066990 8.448000 6.234750
st 4.095880 2.490110 6.237170
st 3.324740 7.046450 0.839732
st 0.717297 8.490300 0.870192
st 0.830225 2.515690 0.793637
ob 1.463210 3.781760 4.625190
ob 2.764240 3.176920 6.929140
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How to setup a multiple potential model
The multiple potential feature is only applied to PDB and xyz input files.
DL_FIELD provides simple procedures to setup models that use more than one potential scheme. First of all, the keyword multiple must be used instead of any specific FF scheme in the DL_FIELD control file. Then specify the potential schemes in the input configuration file.
Example below shows how you can set up a multiple potential model using an input file in the PDB format. The system contains two different molecular structures. One is an ethanol molecule and the other is sulphur hexafluoride.
REMARK An example file using multiple potential.
CRYST1 37.540 37.540 21.842 90.00 90.00 120.00 P1
# POTENTIAL charmm36_cgenff
ATOM 1 C2 ETOH 1 0.995 0.329 -0.000 ALC
ATOM 2 H21 ETOH 1 1.844 -0.392 0.000 ALC
ATOM 3 H22 ETOH 1 1.096 0.975 -0.902 ALC
ATOM 4 H23 ETOH 1 1.096 0.976 0.901 ALC
ATOM 5 C1 ETOH 1 -0.340 -0.404 0.000 ALC
ATOM 6 H11 ETOH 1 -0.456 -1.038 0.907 ALC
ATOM 7 H12 ETOH 1 -0.457 -1.039 -0.907 ALC
ATOM 8 HO1 ETOH 1 -2.235 0.073 0.000 ALC
ATOM 9 O1 ETOH 1 -1.394 0.538 -0.000 ALC
# POTENTIAL opls2005
ATOM 2017 S SHEX 1 16.570 1.991 20.140 1.00 0.00 SF6 S
ATOM 2018 F SHEX 1 15.606 3.062 19.528 1.00 0.00 SF6 F
ATOM 2019 F SHEX 1 17.389 3.127 20.838 1.00 0.00 SF6 F
ATOM 2020 F SHEX 1 17.532 0.920 20.752 1.00 0.00 SF6 F
ATOM 2021 F SHEX 1 17.491 2.100 18.880 1.00 0.00 SF6 F
ATOM 2022 F SHEX 1 15.750 0.855 19.442 1.00 0.00 SF6 F
ATOM 2023 F SHEX 1 15.648 1.882 21.400 1.00 0.00 SF6 F
ATOM 2024 S SHEX 2 1.205 2.521 0.264 1.00 0.00 SF6 S
ATOM 2025 F SHEX 2 1.943 3.523 1.213 1.00 0.00 SF6 F
ATOM 2026 F SHEX 2 0.697 1.717 1.506 1.00 0.00 SF6 F
ATOM 2027 F SHEX 2 0.468 1.519 -0.686 1.00 0.00 SF6 F
ATOM 2028 F SHEX 2 2.488 1.627 0.210 1.00 0.00 SF6 F
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The system contains two different potential schemes: CHARMM36_prot and OPLS2005. The positions of the POTENTIAL directives define the extent of the FF applications. CHARMM36 applies to the ethanol molecule, whereas, OPLS2005 applies to sulphur hexafluoride molecules. The residue labels ETOH and SHEX are the residue labels, of which the MOLECULE templates were predefined in the respective FF library files.
The labels ALC and SF6 are called the Molecular Group names and DL_FIELD will show this as the molecule directives in the dl_poly.FIELD file during the FF conversion.
Warning
It is not common to setup simulation models that contain different FF schemes, unless the different FF schemes are of the same type. For instance, CHARMM36_prot can be mixed with CHARMM36_lipid. Otherwise, user’s discretion is needed. However, multiple potential models are more commonly used for systems containing organic or biological and inorganic elements.
Example below shows how to use the multiple potential scheme in the xyz format for a system contains the organic and inorganic components. It is a system consists of a montemorillonite clay mineral with a benzene molecule. The organic molecule is assigned to the CHARMM22 force field, whereas, the CLAYFF force field is used for the mineral.
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CRYST1 83.908 20.7302253 17.9859383759 90.00 90.00 90.00 (P 1)
# POTENTIAL CHARMM22_prot MOLECULAR_GROUP ORG
C 10.000000 1.390000 0.000000
C 10.000000 0.695000 1.204000
C 10.000000 -0.695000 1.204000
C 10.000000 -1.391000 0.000000
C 10.000000 -0.695000 -1.204000
C 10.000000 0.695000 -1.204000
H 10.000000 2.450000 0.000000
H 10.000000 1.225000 2.123000
H 10.000000 -1.226000 2.122000
H 10.000000 -2.451000 0.000000
H 10.010000 -1.226000 -2.122000
H 10.000000 1.225000 -2.122000
# POTENTIAL inorganic_clay MOLECULE_KEY CLYF MOLECULAR_GROUP clay
Si -2.675000 -6.024000 4.703000
Si -2.700000 -6.039000 -4.313000
Si -2.776000 -3.444000 -8.761000
Si -2.686000 -0.853000 4.722000
Si -2.697000 -0.830000 -4.318000
Si -2.786000 -8.616000 -8.741000
Si -2.690000 -3.463000 6.268000
Si -2.730000 -8.634000 6.283000
Si -2.722000 -8.677000 0.254000
O -3.091000 -4.823000 0.879000
O -3.276000 -2.187000 -7.966000
O -3.282000 -7.370000 -7.946000
O 1.050000 3.459000 -2.711000
Al 0.010000 5.114000 3.217000
Al -0.035000 -0.043000 -5.796000
Al 0.053000 -0.112000 3.283000
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Note that by using inorganic force field scheme would need an additional directive, which in this case, is MOLECULE_KEY CLYF. This provides additional information for DL_FIELD to look for the specific MOLECULE template as defined in the corresponding library file for inorganic_clay FF, or the DLPOLY_INORGANIC_CLAY.sf file.