6.10. MD menu

It is a menu on the molecular dynamics method.

Also, with almost every feature CygwinWM is required.

6.10.1. Solvate/Build Cell

This function is mainly used for the following two purposes.

  1. Arrange solvent molecules around the molecules displayed in the main window

  2. 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_tmp added to the end of the current file name is created, and processing using Packmol is performed in that folder.

Details are described in packmol.bat and packmol.log under the working folder. output.pdb under 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 File

Add molecules from a previously saved molecular structure file to the system. After pressing the button, specify the location of the file and enter the number of molecules to add. If the number of molecules to be added is 1, specify whether the molecules are to be placed randomly or fixed to the coordinates written in the file. When placing a ligand molecule cut from a PDB file, the placement is usually fixed. When performing MD calculations using point charges (RESP charges, etc.) obtained from QM calculations, etc., the file specified here must contain information on the point charges. The point charge information can be maintained in mol2, wmm, or other formats.

Add SMILES

Specify the type of molecules you want to arrange in SMILES format.

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.

Delete

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 Margin 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.

Same as main window

Sets the lattice constant of the cells displayed in the molecular display area.

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.

Option
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
Tolerance

Specify tolerance parameter of Packmol.Specifies the minimum distance between atoms.

Tolerance(Fixed)

Specifies the minimum distance between atoms and the tolerance parameter in Packmol for molecules with Fixed Position. This is useful when you do not want to place solvent in a slab or protein.

Margin

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.

Do not rotate

Align molecules without changing their orientation. It is intended for the creation of nematic liquid crystal phases, etc.

Automatically change random seed every time

The seed of random number when using Packmol is automatically changed every time.

Use PBC if Margin=0 and Packmol supports it

When using CygwinWM 2025/7/1 version or later, if Margin is 0, the molecules are placed considering the periodic boundary condition. If not checked, there will be no molecules that straddle cell boundaries. This feature is not available for Packmol in CygwinWM prior to the 2025/7/1 version.

SMILES converter

Specify the program to use when turning SMILES entered in Add SMILES into a 3D structure.

Shift origin to cell center

Sets the origin to the center of the cell.

Reset

Resets the settings in this window.

Build (Multi)

Create simulation cells according to the settings in this window. Multiple patterns are generated with different random seeds. The random seed used is the value of Random seed in the first structure, the value of Random seed plus one in the second structure, and the value of Random seed plus two in the third structure. The third structure uses the value of Random seed plus two (as below). This is useful to increase the number of samplings by performing multiple MD calculations with different initial coordinates using the structure scan.

Build

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 Import File.

Basic operation is the same as Solvate/Build Cell.

6.10.3. Assign Charges Automatically

Automatically assign charges to multiple molecules.

A working folder with _charge_tmp at the end of the current filename is created and processed. See Use AM1-BCC/Gasteiger charges , Use RESP charges , Use OPLS-AA charges for more details.

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.

Method

Select the method to assign the charge.

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

6.10.4.1. Use AM1-BCC/Gasteiger charges

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_tmp appended at the end of the current file name is created and processed in that. Details are listed on temp.sh, temp.log under working folder. The value of the charge written in the working folder below input.acpypeinput_GMX.itp will be the result.

6.10.4.2. Use RESP charges

Calculate RESP charge using GAMESS. See RESP Charges for details. The GAMESS keywords (including basis functions and calculation methods) and the number of parallels are set in the Tools ‣ Preferences menu Keywords for automatic RESP charge calculation (GAMESS) and :guilabel:` Number of parallels for automatic RESP charge calculation with GAMESS` on the Calculation tab of the Calculation.

6.10.4.3. Use OPLS-AA charges

Use mktop to calculate OPLS-AA charges

6.10.5. Polymer

6.10.6. Interface Builder

6.10.7. Replace Molecules

Replaces all molecules of the specified molecular species with other molecules. Please save the newly placed molecule (one molecule) in wmm or mol2 format before calling this function.

6.10.8. 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.

Neutral

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.

Concentration

Specify the concentration of ion to be substituted.

Cations/Anions

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.

Execute

Run gmx genion on Cygwin. A working folder with the file name _genion_tmp at the end of the current file name is created and processed in that. Details are described in temp.sh, temp.log under 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_tmp in the working folder.

6.10.9. LAMMPS

6.10.10. Gromacs

6.10.11. MODYLAS

MODYLAS Configure, calculation execution, animation display, energy display.

Basically it behaves similarly to MD ‣ Gromacs menu.