Amber masthead
Filler image AmberTools20 Amber20 Manuals Tutorials Force Fields Contacts History
Filler image

Useful links:

Amber Home
Download Amber
Installation
News
Amber Citations
GPU Support
Intel Support
Updates
Mailing Lists
For Educators
File Formats
1 Building Systems
  Simulations of a room-temperature ionic liquid
 
 

1.9 Simulations of a room-temperature ionic liquid

Formerly known as "Tutorial: A room-temperature ionic liquid"

By Chris Lim and David A Case


Creating initial structures

1.1 Drawing the molecules using xleap

1.2 Creating a pdb file

1.3 Repeat

Antechamber

2.1 Generate mol2 and frcmod files for the Acetonitrile:

2.2 Problems with boron

2.2.1 Run antechamber without the charge model

2.2.2 Edit the mol2 file

2.3 Next, go to xLEaP and put in:

Parmchk

Repeat this step for the two remaining mol2 files. You can get the frcmod files we created here: frcmod.acn, frcmod.bmi, and frcmod.bf4. Compare them to the ones you have created. Note that the frcmod.acn file is essentially empty, since all of the parameters needed for that molecule were present in the gaff.dat file. You can get rid of this file if you want.

Packmol

  1. Download Packmol from http://www.ime.unicamp.br/~martinez/packmol/ and follow the installation instructions.
  2. Create an input file named input.inp. Here is an example:
  3. Run Packmol
  4. View the pdb file generated by packmol in Visual Molecular Dynamics (VMD):

Using tLEaP to generate Amber prmtop file

  1. Create an input file, commands.in:
  2. Run tLEaP with input file:

Performing minimization with Sander

  1. Create a script named runmin.sh. This script will create the input file and run sander. “imin=1” tells sander to run minimization, “ntpr=100” saves the restart file every 100 steps, “ntwx=100” prints the trajectory every 100 steps, “maxcyc=10000” runs minimization for 10000 cycles, and “ntb=1” specifies periodic boundary conditions.
    1. Note: Make sure you modify the arguments for sander if you want to run a second simulation. For example, after “min1” finishes, the input coordinate file should be “min1.x”, and the other output files should begin with “min2”.

Running Molecular Dynamics

  1. Create script file named runmd.sh

Imaging with ptraj

  1. First, analyze the Density to see if the average density is close to your target.
  2. To graph density data with xmgrace:
  3. To calculate the average density, examine the sets in xmgrace, or run the following script:
  4. Examine the Energy Total to see if the system is at equilibrium.
  5. Once the density is at target and total energy is at equilibrium, calculate Radial Distribution Functions.
    1. In this case, the average density is 1.0774 cc/mol, whereas the paper's density is 1.087 cc/mol.

Self-Diffusion Coefficients

9.1 Create the input file

9.2 Run ptraj

9.3 Run gnuplot

9.4 Calculate

Conclusion