<img src="ser_lys_fe0.6_gmin.png" width="50%", height="50%">
This set of examples explore applying A12GMIN to find the potential and free energy global minima for the SER-LYS dipeptide.
As a prerequisite, you will need to have compiled A12GMIN (or have access to binary).
Unfortunately due to licensing restrictions, we are not able to distribute the source code for (A9/A12)GMIN or (A9/A12)OPTIM. If you have an AMBER license - please contact David Wales to request access to the AMBER specific source code.
If you have the source code, all should compile fine using gfortran and cmake.
Visualisation is done with both gnuplot and VMD which can be obtained here
These examples are practically focussed and as such, we won't be covering the theoretical basis of basin-hopping or how the free energy is calculated.
Each example is stand-alone - you do not need to do them in order, although it may aid understanding to do so. Expected output is provided for each, but bear in mind that it may not match yours 100% of the time.
Where appropriate, annotated versions of input files are provided (FILE_annotated) describing their contents. These descriptions are not exhaustive so for more detail, see the documentation.
Covers the basics of using A12GMIN for the SER-LYS dipeptide, including:
- running basin-hopping to find the the 20 lowest energy minima
- tracking the progress of a basin-hopping run using gnuplot
- visualising the minima found using VMD or Pymol
Demonstrates the free energy basin-hopping approach including:
- comparing the potential and free energy global minima
- investigating the effect of raising the temperature on the global free energy minimum