Lesson 1 -- How to create a new input file for the Sander minimization

Objective: The minimization method is applied to optimize the building model or used to relax the system before the molecular dynamics. The Sander_GUI can prepare and save input files for the minimization

Prerequisite: For Sander minimization, the input file, toplogy file and coordinate file are needed. So prior to minimization 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 minimazation

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

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

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 minimization in “run type” section

3. Click on the “minimization” button, choose one method of minimization in the “minimization type” section, there have three minimization types: steepest descent, conjugate gradient, and combination of steepest descent and conjugate gradient. Then Input the parameters of initial step length, number of cycles, maximum step length, convergence criteria for RMS of gradient and switch to conjugate gradient after step, 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 Periodic boundary condition model, select the “Periodic” button, and then choose the Ewald type in the “Ewald type” section. The periodicity use the constant volume for the minimization normally. Input 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 parameters or use the default parameters. If need to restraint some atoms in minimization process, you can choose the “fix coordinates” button or “restrain coordinates” button. Then click the “constraints” button input the restrain atom group

5. If need to restraint some atoms in minimization process, you can choose the “fix coordinates” button or “restrain coordinates” button. Then click the “constraints” button input the restrain atom group.

6. Click on the “I/O” button, input the output frequency of the energy in the “program output” section. 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 "View Input" button in order to have the input run. Save the input file as “min.in”. The preparation of input file for minimization is done

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

polyA_T_min.in: The input file of GB model for the polyA-T minimazation