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This example shows the implementation of the potential of mean force (PMF) calculation in SDA 7 with a system of a three-histidine tripeptide (3HIS) tripeptide on an Au(111) surface. Details are given in : Ozboyaci, M., Martinez, M. and Wade, R.C. An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association.J. Chem. Theory Comput. (2016), 59:7598-7616. 10.1021/acs.jctc.6b00350

The PMF code has been implemented in SDA 7 and tested only for ProMetCS force-field (See aubs example).

Directory description

This example can be found in directory examples/au3his/.

prepare_grids_and_ecm/ Directory for generating grids and effective charges needed for running the simulation
data_grid/ Data files (pdb and input files) needed for running the examples
run_hits/ Results of the example run script for protein-metal surface docking
run/ Directory to run the PMF calculations
doc/ This documentation
Input parameters

A number of sampling parameters should be given in the input file. Refer to the input page for detailed descriptions of the parameters.

Running examples

Assure you have compiled all the executables and tools in sda_flex/bin/ first or refer to the compilation section.

First, run the script run-au3his_ed_hd_ecm_lj.sh from the prepare_grids_and_ecm/ directory to generate the grids necessary for this example.

Then go into the run/ directory that contains the input file and run the shell script

For the PMF calculations :

cd run/

You can check that output files are similar to the ones generated in the *_hits directory.
PMF profile of the 3HIS-Au(111) adsorption

Calculations will produce a file called pmf.dat that contains the PMF values at the distances from the surface based on the dz value.
Using gnuplot plotting program with the input file make_plot.gp a graphics file named pmf_au3his.eps will be obtained. Using a graphics viewer that supports EPS format, the following figure can be obtained.

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