Adding solvents¶
The DL_FIELD control file also contain a feature where you can solvate your system. This is done once the FF model for the input structure has been setup. If the Solution Maker feature is activated, then the system will only be solvated after molecules have been duplicated.
Prior to solvation, the whole molecular system is considered to be the solute unit. This also includes solvent molecules that have been included in the user input configuration file.
The necessary input parameters are as follows:
solvent_key cutoff FF_scheme
where solvent_key is the name of the molecule that will fill the system. The cutoff value is the minimum permitted distance between a solvent molecule and a solute molecule. The solvent molecule will be rejected if the distance is smaller than the cutoff value.
The FF_scheme indicates the type of FF scheme for the solvent. DL_FIELD will use this information to look for the solvent MOLECULE according to the FF scheme.
For example:
meoh 2.0 cvff
Means solvate the system with methanol with a cutoff distance of 2.0 Angstrom. The FF model for the solvent would be the CVFF.
DL_FIELD also recognise the command default for the FF_scheme. It means the FF scheme for the solvent would be the same as what’s been specified in the control file.
Note
Solvation feature only works if simulation box size is specified and must be either cubic or orthrhombic shapes. In addition, DL_FIELD can only solvate systems of sizes that are at least 20 Angstrom at all x, y, and z directions.
Solvent templates
DL_FIELD uses solvent templates to solvate the system. These templates are located in the solvent/ directory. Each template consists of a box of pre-equilibrated solvent molecules at the standard density at 300 K. The template size is 20 x 20 x 20 Angstrom 3.
To find out what solvent templates are available, look into the file called solvent_list in the solvent/ directory. Under the Solvent list tile, the following information is displayed:
solvent_key - description - filename
Below shows a portion of the solvent list:
# Water
TIP3P_O - Original TIP3P - water_tip3p_o
TIP3P_C - Charmm-specific TIP3P model - water_tip3p_c
TIP3P_E - TIP3P water model optimised for ewald sum - water_tip3p_e
TIP4P - TIP4P water model (one pseudo point) - water_tip4p
TIP5P - Five-site water model (two pseudo points) - water_tip5p
TIP5P_E - Five site water model optimised for ewald sum - water_tip5p_e
SPC - SPC water model - water_spc
SPCE - SPC/E water model - water_spce
WATER_PCFF - Water model specific to PCFF - water_pcff
# Alcohol
MeOH - Methanol, obtained from CHARMM FF - methanol
EtOH - Ethanol, from OPLS2005 - ethanol
IPA - Isopropyl alcohol (propan-2-ol), from CHARMM FF - ipa
..
..
The most relevant information to the users are solvent_keys. For example, to use original TIP3P water model, insert the key TIP3P_O in the control file. To use methanol as solvent, insert the key MeOH in the control file. Note that the solvent_keys are case insensitive.