Lesson 2 -- How to create a new input file for the Sander molecular dynamics!

Objective: The molecular dynamics stimulation is applied in the model optimization, conformation sampling and energy analysis. This Sander_GUI can prepares and save input files for the molecular dynamics

Prerequisite: For Sander molecular dynamics, the input file, toplogy file and coordinate file are needed. So prior to MD calculations, the users should use xleap prepare the topology file and coordinate file. And use Sander GUI prepare the input file.  

• polyA_T_GB.inpcrd: The coordinate file of GB model for the polyA-T MD

• polyA_T_GB.prmtop: The topology file of PBC model for the polyA-T MD

• polyA_T_pbc.inpcrd: The coordinate file of GB model for the polyA-T MD 
• polyA_T_pbc.prmtop: The topology file of PBC model for the polyA-T MD 

Procedure: In the Sander GUI, enter the following information in the appropriate place:

1. Input your research title in the “title” section

2. Choose the Molecular Dynamics in “run type” section

3. Click on the “Molecular Dynamics” button

   1. choose one mode of molecular dynamics in the “Mode” section, there have two type of molecular dynamics mode: initial run and restart/continuation
   2. choose one stimulation ensemble (constant energy and constant temperature) from the “ensemble” section. If choose the constant temperature ensemble, there have three temperature control methods: Weak-coupling algorithm, Andersen temperature coupling scheme and Langevin dynamics control. Select one temperature control method from the “Temp control” section
   3. Then Input the parameters of molecular dynamics, or use the default parameters

4. Click on the “potential function” button choose the potential function type (Periodic boundary condition model and Generalized Born model)

   1. If use the periodic boundary condition model, select the “Periodic” button, and then choose the Ewald type in the “Ewald type” section. From “periodicity” button choose one periodic boundary condition (constant volume or constant pressure). If choose the constant pressure boundary condition, then select one pressure control method (isotropic and anisotropic) from the “pressure scaling” button. Input all the parameters or use the default parameters
   2. If use the Generalized Born model, don’t select the “Periodic” button. Choose the Generalized Born model in the “GB type” section, Then input the corresponding parameters or use the default parameters
5. If need to restraint some atoms in molecular dynamics process, you can select the “fix coordinates” button or “restrain coordinates” button. Then click on the “constraints” button input the restrain atom group
6. Click on the “I/O” button, input the parameters in the “program output”, “print of averages”, “trajectory of coordinates”, “trajectory of velocities”, “coordinate restart” and “trajectory of energies” sections or use the default parameters. Click on the “Browse” button of “input coordinates” section input the coordinate file. Click on the “Browse” button of “input parameter/topology” section input the topology file
7. If all above input sections are finished, then click on the "View Input" button in order to have the input run. Save the input file as “md.in”. The input file preparation of molecular dynamics is done

Notes:  There is a example for the Sander MD input file.

        polyA_T_md.in: The input file of GB model for the polyA-T MD