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