Command Line GUIΒΆ

Tinker programs can take interactive input. The prompt messages try to be self-explanatory. Following is an example to use the interactive interface for a short DHFR simulation with an AMOEBA force field.

Warning

The simulation will not run unless more keywords are added to the key file. This is only a demonstration to the interactive interface.

Item

Value

Input

Coordinate File

dhfr2.xyz

dhfr2.xyz

Simulations Steps

1000

1000

Time Step

2 fs

2

Time Between Saves

1 ps

1

Ensemble

NVT

2

Thermostat Temperature

298 K

298

zw@Blade:~/tutorial/example$ tinker9 dynamic

     ###############################################################
   ###################################################################
  ###                                                               ###
 ###        Tinker9  ---  Software Tools for Molecular Design        ###
 ##                                                                   ##
 ##                    Version 1.0.0-rc   Jan 2021                    ##
 ###                       All Rights Reserved                       ###
  ###                                                               ###
   ###################################################################
     ###############################################################
 Compiled at:  20:54:14  Feb  3 2021
 Commit Date:  Wed Feb 3 20:52:06 2021 -0600
 Commit:       3b0791c0


 Enter Cartesian Coordinate File Name :  dhfr2.xyz

 ################################################################
 Joint Amber-CHARMM Benchmark on Dihydrofolate Reductase in Water
 23558 Atoms, 62.23 Ang Cube, 9 Ang Nonbond Cutoffs, 64x64x64 PME
 ################################################################

 Enter the Number of Dynamics Steps to be Taken :  1000

 Enter the Time Step Length in Femtoseconds [1.0] :  2

 Enter Time between Saves in Picoseconds [0.1] :  1

 Available Statistical Mechanical Ensembles :
    (1) Microcanonical (NVE)
    (2) Canonical (NVT)
    (3) Isoenthalpic-Isobaric (NPH)
    (4) Isothermal-Isobaric (NPT)
 Enter the Number of the Desired Choice  [1] :  2

 Enter the Desired Temperature in Degrees K [298] :  298

Once you are familar with the interactive interface, you can simply append the interactive input to the program name.

zw@Blade:~/tutorial/example$ tinker9 dynamic dhfr2.xyz 1000 2 1 2 298

     ###############################################################
   ###################################################################
  ###                                                               ###
 ###        Tinker9  ---  Software Tools for Molecular Design        ###
 ##                                                                   ##
 ##                    Version 1.0.0-rc   Jan 2021                    ##
 ###                       All Rights Reserved                       ###
  ###                                                               ###
   ###################################################################
     ###############################################################
 Compiled at:  20:54:14  Feb  3 2021
 Commit Date:  Wed Feb 3 20:52:06 2021 -0600
 Commit:       3b0791c0


 ################################################################
 Joint Amber-CHARMM Benchmark on Dihydrofolate Reductase in Water
 23558 Atoms, 62.23 Ang Cube, 9 Ang Nonbond Cutoffs, 64x64x64 PME
 ################################################################

You can also use stdin redirection to run Tinker programs. Save the command line arguments in a file and use it as follows.

zw@Blade:~/tutorial/example$ cat args.txt
dhfr2.xyz
1000
2
1
2
298
zw@Blade:~/tutorial/example$ tinker9 dynamic < args.txt