6.10. MD menu¶
It is a menu on the molecular dynamics method.
MD pack is necessary to use the function of MD menu. Also, with almost every feature CygwinWM is required.
6.10.1. Solvate/Build Cell¶
This function is mainly used for the following two purposes.
- Arrange solvent molecules around the molecules displayed in the main window
- Create liquid phase by arranging low molecules
There are three kinds of molecules that can be arranged as follows.
- Molecule displayed in the main window
- Molecules preserved in mol 2 format
- water molecule
A working folder with
_builder_tmpadded to the end of the current file name is created, and processing using Packmol is performed in that folder.
Details are described in
packmol.logunder the working folder.
output.pdbunder the working folder is the file containing the final generated molecular structure.
- Add Displayed Molecule
- Add molecules displayed in the main window. After pressing the button, enter the number of molecules to be added. If only one is placed, other molecules are aligned with the coordinates fixed for the molecules displayed in the main window.
- Add Water
- Add water molecules to the system. After pressing the button, enter the number of molecules to be added. The water molecule model is selected from Water Model in Options tab.
- Add .mol2 File
- Add molecules previously saved in .mol2 format to the system. After pressing the button, specify the location of the .mol2 file and enter the number of molecules to be added. If the number of molecules to be added is 1, specify whether to randomly arrange the molecule or to fix it at the coordinates written in the .mol2 file. When arranging ligand molecules cut out from a PDB file, it is usually fixed. When executing MD calculation using point charge (such as RESP charge) obtained from QM calculation etc., the point charge information must be described in the .mol2 file specified here.
- Deletes the selected item in the above list.
- Simulation Cell
- Set Density
- Specify the density of the simulation cell to be created. If it is too large, you may not be able to insert the molecule sufficiently, so in case of liquid phase it is usually set to about 0.5~0.8 g/cm 3.
- Set Distance from Solute
- When choosing Solvate for Method, specify the distance between the molecule displayed on the main window and the simulation cell.
- Set Lattice Constants
- Specify the size of the simulation cell directly. When you press : guilabel:Same as main window button, the same value as the cell set in the main window is entered.
- Change only one direction
- Used to move one lattice constant to the specified density while keeping two lattice constants fixed. It can be used by selecting triclinic in Box Type. This is especially useful when creating interface structures.
- Box Type
- Specify the shape of the simulation cell.
- Water Model
- Specify the water model added by Add Water. The coordinate data of the specified water model will be quoted from the library of the topology file installed in Gromacs on Cygwin.
- Packmol Parameters
- Specify tolerance parameter of Packmol.
- Specify the width of the area where no atoms are placed near the edge of the cell when using Packmol.
- Random seed
- Specify the seed of random number when using Packmol.
- Automatically change random seed every time
- The seed of random number when using Packmol is automatically changed every time.
- Resets the settings in this window.
- Create a simulation cell according to the contents set in this window.
6.10.2. Insert Molecules¶
You can add multiple molecules stored in mol 2 format to the structure displayed in the main window. If no simulation cell has been created, create it with Create/Edit Cell or Solvate/Build Cell beforehand.
If you want to add only one additional molecule without changing the coordinates, please select Append.
The internal operation is the same as Solvate/Build Cell.
6.10.3. Assign Charges Automatically¶
Automatically assign charges to multiple molecules.
A working folder will be created with the current file name suffixed with
_charge_tmp, and processing using Packmol will be performed in it.
- Set … for all components
If checked, charges will be calculated for all molecular species displayed in the main window using the method specified in the pull-down menu. If unchecked, select a Method for each atomic species.
- Except for components that are already charge
- If checked, even if Set … for all components is checked, no new charge will be assigned to molecules that have already been assigned.
- Except for protein, monoatomic ion and water
- When checked, no charge is assigned to proteins, monatomic ions, and water molecules in this function. In the MD calculation of proteins, it is necessary to check the box because it takes time to calculate the charge by methods such as AM1-BCC and the charge is automatically assigned from the residue name when assigning the force field.
- Select the method to assign the charge.
- Set the charge for that molecular species. The charge is specified as 0 for neutral molecules and +1, -1 for ions.
6.10.4. Assign Charges Manually¶
188.8.131.52. By Acpype¶
Calling this function while only one molecule is displayed in the main window allocates point charge to each atom by AM1 - BCC or Gasteiger method. Internally I use the Acpype program on Cygwin. It is used when creating a file in mol 2 format to be inserted by charge allocation of solute molecules or Solvate/Build Cell or Insert Molecules. When allocating charge to non-neutral polyatomic ions, it is necessary to use RESP charge or this function. For polyatomic ions, enter the charge into Total charge [e]. A working folder with the
_acpype_tmpappended at the end of the current file name is created and processed in that. Details are listed on
temp.logunder working folder. The value of the charge written in the working folder below
input.acpypeinput_GMX.itpwill be the result.
184.108.40.206. By Manual Entry¶
You can directly specify the point charge value for each atom type for the molecular (crystal) structure displayed in the main window. It is mainly for solid system.
6.10.7. Generate Ions¶
Replace water molecules with monoatomic ions. It is necessary to arrange water molecules in the system in advance. To place water, use Solvate/Build Cell. It is mainly used to neutralize the charge in the system in protein systems. Internally run gmx genion on Cygwin.
- In the case of True, we arrange the ions so that the charge of the whole system becomes neutral, and Number of Cations and Number of Anions are ignored. In the case of False, the number of ions described in Number of Cations and Number of Anions are respectively allocated.
- Specify the concentration of ion to be substituted.
- Specify the type of cations and anions from the pulldown.
- Number of Cations/Number of Anions
- Specify the number of cations and anions. This setting is valid when Neutral is False.
- Run gmx genion on Cygwin. A working folder with the file name
_genion_tmpat the end of the current file name is created and processed in that. Details are described in
temp.logunder the work folder. On the way, automatic creation of a temporary topology file (
temp.top) may fail if the molecules in the system are inappropriate. Details of the topology file creation are output in
temp_top_tmpin the working folder.