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Overview

FHedin edited this page Mar 3, 2017 · 1 revision

Overview of the workflow for the current version

Welcome screen

At initial run, welcome screen for choosing what to do

fig0

MTP parameters from Ab Initio

Loading coordinates

First selection in welcome screen gives access to the Gaussian optimization procedure, where first a molecule is loaded :

fig1

MTP fit

Then after success of the Ab-Initio calculation the user defines initial charges for the atoms, chooses fit parameters and runs the optimization.

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After a short time a table displays the results :

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It is then possible to go to the CHARMM fit section by using the bottom right button.

CHARMM fitting procedure

From the Welcome screen user can access directly to the CHARMM fitting procedure (useful if the previous section was already performed before). Otherwise the screen is the next step reached in the workflow :

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Generating input files

Then input files can be generated, and they are displayed in several tabs, and if required the user can review and edit some of those files. When ready the user can submit all the simulations by pressing the bottom right button that will internally call all the required scripts :

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Visualizing output files

If for some reason simulation failed an error window appears where the user can visualize failing output files :

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Otherwise at the end of all simulations the user gets a successful run window :

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Obtaining thermodynamic properties

Then output files are parsed for extracting for extracting Temperature, molar mass and number of residues and then the density, Enthalpy of Vaporization and Free Energy of Solvation are estimated :

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Analyze CHARMM output files

All the output files from a given simulation are stored in the data directory (it possible to change the path of this directory and its name from the config_gui.ini file). By choosing the option Analyze CHARMM output files from the main window it is possible to reload existing output files from a subdirectory of data. Once loaded the files will bring the user again to the window for obtaining again all the estimated properties.

fig17

Running a set of CHARMM simulations with altered PAR and TOP files

Define list of scaling parameters

The third possibility in Welcome screen gives the user the possibility to generate a set of scaled PAR and TOP files for CHARMM where the LJ parameters sigma and epsilon are scaled : the user first chooses how many modifications to perform :

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Then the user chooses the scaling parameters :

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Save all files and run all simulations

Then it is possible to save all those files an to run all simulations :

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Generating custom PSF and TOP files using a XYZ file

The fourth possibility in Welcome screen gives the user the possibility to generate a set of custom topology (TOP,RTF) and structure (PSF) files.

Those files are specifically generated for the studied molecule, using the optimised XYZ coordinates from the Gaussian simulation.

Once generated the files are displayed in a tabs structure so the user still has the possibility to complete the generated files.

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