Protein Structure & Molecular Modeling lab
Institute of Biosciences & Applications
NCSR "Demokritos", 15310 Ag. Paraskevi-Athens, Greece

 

Gromita Help

Introduction

GROMITA-4.6 is an update of the GROMITA-GUI, compatible with GROMACS v.4.6.x. It is written in perl making extensive use of perl/tk achieving portability in a wide variety of operating systems and architectures. GROMITA provides friendly to use buttons in a windows-based environment while maintaining a terminal mode for the experienced user

 

Contents

1. Prerequisites
2. Installation
3. Description
4. Shortcuts
5. Getting started
6. GROMACS to GROMITA migration guide
7. FAQ
8. Troubleshooting
9. Acknowledgments

1. Prerequisites

1.a Hardware

Any computer capable of running GROMACS can run GROMITA. A large screen (17') is preferable with high resolution, but not necessary

1.b. Software

GROMITA is compatible with any *NIX type OS. It only needs an installation of Perl (usually installed in most unix distributions) and perl/Tk a module available from CPAN. In order to perform molecular dynamics GROMACS and the programs it depends on must be installed.

 

2. Installation

GROMITA can be easily installed with the setup.pl installation perl script, which checks if all prerequisites are available and installs gromita.

  1. Install GROMACS and the programs it depends on
  2. Install Perl (in most Linux distributions it should be already installed)
  3. Install Perl/Tk using the CPAN module
      Make sure that the CPAN module is installed
      $>perl -e 'use CPAN;'
      if it is installed, no error message should appear.
      Switch user to root in order to make available perl/tk for all users and invoke a CPAN shell
      $>su
      Password:
      #>perl -MCPAN -e shell
      (if you are using Ubuntu type instead: $>sudo perl -MCPAN -e shell and type your user password, not the root)
      install Perl/Tk:
      $>cpan>install Perl/Tk
      some installation and testing messages will follow, and when complete type quit to exit the CPAN shell
  4. Extract the compresed file (e.g in your desktop)
  5. Open a terminal and cd to newly created directory
  6. In order to have GROMITA available for all users and have the mspc option working you must install GROMITA as root
    7. $>su
    Password:
    #>perl setup.pl
    Note: If you are using Ubuntu, instead of the above type $>sudo perl setup.pl and when prompted enter your password (not the root)
  7. run the setup script:
    8. The setup script will check for the installed perl version, its modules, gromacs path e.t.c. Follow the instructions. Note that GROMITA may complain about some version numbers, because it asks for the versions under which it was developed. It will probably work well with much lower versions, just it has not been tested with them.
    $>perl setup.pl
    checking perl version...ok
    checking for required perl modules:
    File::HomeDir: ok
    File::Spec: ok
    Time::HiRes: ok
    Carp: ok
    Tk: ok
    searching for GROMACS...ok
    counting processors...1
    searching for GROMACS dependences...FFTW: ok

    SETUP SUMMARY
    -----------
    Nothing missing
    Proceed with gromita installation? [y/n] 

  8. When checking for installed programs is finished the installation script will ask for verification before proceeding. Note that the following steps must be done as root (superman) for GROMITA to be available to all users:
    9. Proceed with gromita installation? [y/n] y
    Starting installation
    Installation completed!
  9. GROMITA is ready! Just type gromita and it will load

 

3. Description

GROMITA's main window is seen in the following screenshot. Its main parts is a Menubar, the Main Buttons on the left side of the screen, the Output Window on top, the Command Line Window bellow and the Indicators Bar.

Screenshot-Gromita

A. Menubar

File

The File menu contains the basic options for file handling, logging, printing and ending the program.

  • File Open

Opens a dialog window in order to select a pdb file

  • File Save

Saves a report of work done. If no report have been saved yet it does what a FileSave as would do

  • File Save as

Saves a report (.log file) containing the following information (not necessary all):
a) A title displaying the current date and time
b) The contents of the Command Line Window
c) The contents of the Output Window on top

  • File Close

Closes the currently loaded pdb file

  • File Start/Stop log

By default no logging of Gromita's activities is done. If this option is selected a log file will be created or if it exists, information will be appended to the end of the file. By default the logfile created is named logfile.log. If there is a need of keeping information in a different file a new name can be specified in the Options->Preferences menubutton.

  • File Print

Sends to the default printer a report containing the following information (not necessary all):
a) A title displaying the current date and time
b) The contents of the Command Line Window
c) The contents of the Output Window on top

  • File Quit

Ends GROMITA, but does not interrupt GROMACS if it is still working. It lets it continue working in the background. If there is a need of interrupting some GROMACS process, there is the button Interrupt at the Indicators Bar.

View

  • View Clear screen
    • View Clear screenOutput
Clears the Output Window
    • View Clear screen Command Line
Clears the the Command Line Window
  • View molecule
If a molecular viewer is defined, the pdb file loaded is shown. For defining a viewer see Options->Preferences menubutton

Options

  • Options->Preferences
Opens a dialog window with the customizable values of GROMITA.
  • filenames: GROMITA uses the default GROMACS filenames (pdb2gmx, genbox etc), but also enables the use of custom names.
  • force field paths: The paths were forcefield files are stored. By default the current path and the path where GROMACS is installed
  • path: If defined this path will be prepended to GROMACS programs. This option can be used if GROMACS is not in the system's path
  • terminal: the terminal to be used for andvanced interactive commands. By default it is xterm. For KDE can be changed to Konsole. Any other string besides 'xterm', 'konsole' and 'gnome-terminal' will be used without any further arguments, so a custom program or a different configuration for xterm or konsole can be used. xterm is called with the -hold option, while konsole with -noclose
  • preferred molecular viewer: The name of the preferred molecular viewer for inspecting .pdb files. This entry is used 'as is' in the command line, which means that any argument can be passed to the viewer, or even a path can be prepended
  • logfile: The name of GROMITA's log file.
The window also has three buttons. Save saves the user preferences not only for the current session, but also for future invocations of GROMITA. Restore Defaults restores the default values for all entries.

  • Options-> Terminal mode

Forces advanced mode only for the next command. In terminal mode the output is shown in a terminal window and can be useful in interactive commands. Normaly this option should not be used, when gromita guesses when gromacs will need feedback and automatically runs the command in terminal mode.

  • Options-> Computer load

Opens a window showing the cpu % load for each processor and the overall average

 

 

Trajectory

  • View

Opens a dialog box with options for ngmx trajectory viewer
  • Convert
Opens a dialog box with options for the trjconv trajectory converter

Help

Opens this help file in a web browser.

      B. Main buttons

      Each button presents a basic step of a standard molecular dynamics simulation. By pressing each button a new window appears containing a variety of options. The options are grouped as basic and advanced. In the last row of each window they are three standard buttons OK, Basic/Advanced and Cancel.

      By pressing the OK button the corresponding GROMACS program is invoked with the options activated by the user options. By default the minimum necessary options are activated. Any other option is activated only when the user focus, press or change its value. 

      By pressing the cancel button the window closes without any further action.

      By pressing the Basic/Advanced button the window toggles between the basic and advanced mode hiding or showing the advanced options, respectively.

      Only one window of each main button can be open at any time.

      Generate topology

      Generate topology opens a window enabling the user to add hydrogens create coordinate and topology files from the pdb file loaded. It corresponds to pdb2gmx.

      The basic options include a force field selector, and the filenames of the GROMACS coordinates and topology file. A checkbutton GROMACS help is also available that shows GROMACS help for the specific program in the output window.

      Enlarge box

      In this step a box of water with custom shape and size is defined or modified in which. Corresponds to editconf.

      Solvate protein

      Solvates a molecule in a box of water. Corresponds to genbox.

      Prepare Genion

      Corresponds to grompp.

      Genion

      Corresponds to genion.

      Prepare EM

      Corresponds to grompp, GROMACS preprocessor. In this step the binary files are prepared for Energy minimization.

      Energy Minimization

      The actual energy minimization step. Corresponds to mdrun.

      Prepare MD

      Corresponds to grompp, GROMACS preprocessor. In this step the binary files are prepared for Molecular Dynamics.

      Molecular Dynamics

      In this step the molecular dynamics are run. Corresponds to mdrun.

      C. Output window

      Between the output window and the command line window there is a divider that can be moved (by clicking and dragging the mouse button 1) changing the two windows' relative size.

      output This is a read-only terminal-like window that shows Gromita's actions GROMACS output and some other information. Gromita's actions shown are loading or closing files and GROMACS invocations. A color code highlights GROMACS output warnings and errors which are also summed in a pop-up window.
      moving around

      The output-window has two scrollbars for scanning the text. For fast scanning the text the middle mouse button can be used. The text is "grabbed" and moved around. Keyboard arrow keys, page up and down have their well known function and can also be used for moving around.
      selecting By pressing mouse button-1 and moving the mouse across the output window the text is selected and can be copied to any other application. Pressing shift and moving around with the arrow keys or page up and down can also be used.
      refreshing By default the window will not erase any text, so a great amount of output could fill the memory and slow down the system. Practically this never happens so there is no worry of loosing output information nor downgrading performance. In case there is a need of erasing previous messages View Clear screenOutput should be used.
      advanced features There are some advanced features of the output window, rarely used, but nevertheless could prove very useful in some tasks. Right clicking when the mouse pinter is in the output window pops up a small menu which enables some basic operations. File Exit: For fast quiting Gromita
      Edit Copy: Copy selection
      Edit Select All
      Edit Unselect All
      Search Find: Opens a dialog with options to find text in either forward or backward directions, using exact search or regular expressions and case sensitive or not. It can find only one or all occurrences
      Search Find Next
      Search Find Previous
      View Goto Line...: Move to specified line of the text window
      View Which line: Display line and column of cursor
      View Wrap: Wrap text by word, character or remove word wrapping.

      D. Command Line Window

      This window displays the GROMITA's actions as GROMACS commands in a terminal. Moving around, selecting text, refreshing the contents and its advanced features are as in Output Window.

      E. Indicators Bar

      Shows various status information. From right to left:

      log on/of an indicator of whether a log file of the current actions is kept. Toggles from the menu File Start/Stop log or with the Control+l shortcut.
      cpu % The percentage of cpu usage, refreshing every second. Useful for monitoring long lasting molecular dynamics.
      Interrupt button A button for interrupting the currently running GROMACS program. If GROMACS hangs up or the user wishes to stop a process, by pressing the Interrupt button, a kill signal is sent to to the process. The button is active only when a process is running.
      Progress indicators These indicators are shown only when the verbose option is selected from the Energy Minimization and Molecular DynamicsMain Buttons. There are three progress indicators, a progress bar showing the current step as a fraction of the total steps, a label showing an estimation of time left for the process to finish, and the percentage of it done. Estimations and step count is done by GROMACS.

      4. Shortcuts

      Menubar shortcuts are shown next to each command

      Ctrl + o

      File Open
      Ctrl + s

      File Save
      Ctrl + a

      File Save as
      Ctrl + w

      File Close
      Ctrl + l

      File Start/Stop log
      Ctrl + p

      File Print
      Ctrl + q

      File Quit
      F1 Help


      The shortcuts for output and command line windows are common for both. The following section describes shortcuts and bindings available for these windows as described in Tk::Text documentation:

      In the descriptions below, word refers to a contiguous group of letters, digits, or characters, or any single character other than these.
      1. Clicking mouse button 1 positions the insertion cursor just before the character underneath the mouse cursor, sets the input focus to this widget, and clears any selection in the widget. Dragging with mouse button 1 strokes out a selection between the insertion cursor and the character under the mouse.
      2. Double-clicking with mouse button 1 selects the word under the mouse and positions the insertion cursor at the beginning of the word. Dragging after a double click will stroke out a selection consisting of whole words.
      3. Triple-clicking with mouse button 1 selects the line under the mouse and positions the insertion cursor at the beginning of the line. Dragging after a triple click will stroke out a selection consisting of whole lines.
      4. The ends of the selection can be adjusted by dragging with mouse button 1 while the Shift key is down; this will adjust the end of the selection that was nearest to the mouse cursor when button 1 was pressed. If the button is double-clicked before dragging then the selection will be adjusted in units of whole words; if it is triple-clicked then the selection will be adjusted in units of whole lines.
      5. Clicking mouse button 1 with the Control key down will reposition the insertion cursor without affecting the selection.
      6. The view in the widget can be adjusted by dragging with mouse button 2.
      7. If the mouse is dragged out of the widget while button 1 is pressed, the entry will automatically scroll to make more text visible (if there is more text off-screen on the side where the mouse left the window).
      8. The Left and Right keys move the insertion cursor one character to the left or right; they also clear any selection in the text. If Left or Right is typed with the Shift key down, then the insertion cursor moves and the selection is extended to include the new character. Control-Left and Control-Right move the insertion cursor by words, and Control-Shift-Left and Control-Shift-Right move the insertion cursor by words and also extend the selection. Control-b and Control-f behave the same as Left and Right, respectively. Meta-b and Meta-f behave the same as Control-Left and Control-Right, respectively.
      9. The Up and Down keys move the insertion cursor one line up or down and clear any selection in the text. If Up or Right is typed with the Shift key down, then the insertion cursor moves and the selection is extended to include the new character. Control-Up and Control-Down move the insertion cursor by paragraphs (groups of lines separated by blank lines), and Control-Shift-Up and Control-Shift-Down move the insertion cursor by paragraphs and also extend the selection. Control-p and Control-n behave the same as Up and Down, respectively.
      10. The Next and Prior keys move the insertion cursor forward or backwards by one screenful and clear any selection in the text. If the Shift key is held down while Next or Prior is typed, then the selection is extended to include the new character. Control-v moves the view down one screenful without moving the insertion cursor or adjusting the selection.
      11. Control-Next and Control-Prior scroll the view right or left by one page without moving the insertion cursor or affecting the selection.
      12. Home and Control-a move the insertion cursor to the beginning of its line and clear any selection in the widget. Shift-Home moves the insertion cursor to the beginning of the line and also extends the selection to that point.
      13. End and Control-e move the insertion cursor to the end of the line and clear any selection in the widget. Shift-End moves the cursor to the end of the line and extends the selection to that point.
      14. Control-Home and Meta-< move the insertion cursor to the beginning of the text and clear any selection in the widget. Control-Shift-Home moves the insertion cursor to the beginning of the text and also extends the selection to that point.
      15. Control-End and Meta-> move the insertion cursor to the end of the text and clear any selection in the widget. Control-Shift-End moves the cursor to the end of the text and extends the selection to that point.
      16. The Select key and Control-Space set the selection anchor to the position of the insertion cursor. They don’t affect the current selection. Shift-Select and Control-Shift-Space adjust the selection to the current position of the insertion cursor, selecting from the anchor to the insertion cursor if there was not any selection previously.
      17. Control-/ selects the entire contents of the widget.
      18. Control-\ clears any selection in the widget.
      19. The F16 key (labelled Copy on many Sun workstations) or Meta-w copies the selection in the widget to the clipboard, if there is a selection.


      5. Getting started

      Create a directory in your home or Desktop for working with GROMITA, eg:

      $> mkdir /home/user/work


      change directory to work

      $> cd work


      invoke GROMITA

      $>gromita


        GROMITAis now loaded.

      Go to Options Preferences and type your favourite molecular viewer (e.g. rasmol, pymol) and terminal (e.g. xterm, konsole) for GROMITA to use

      Go to File Open and load a pdb molecule

      Use the main buttons to perform your first simulation

      6. GROMACS to GROMITA migration guide

      GROMACS programGromita's Main Buttons
      pdb2gmx Generate topology
      editconf Enlarge box
      genbox Solvate protein
      grompp Prepare EM
      Prepare MD
      genion Prepare Genion
      Genion
      mdrun Energy Minimization
      Molecular Dynamics
      trjconv View Trajectory
      ngmx Convert Trajectory

      7. FAQ

      1. How can I change the size of the Output window/Command line window?
          With the mouse click and drag the line dividing the output window from the command window
      2. How can I clear the contents of Output window/Command line window?
          Use the menu options View Clear screen
      3. What is the equivalent of a GROMACS command?
          Check the links in the 'GROMACS to GROMITA migration guide' section
      4. How do I become root (switch user)?
          use the command
          su (swich user), and type the root pasword $>su
          Password:
          #>
          If you are using Ubuntu, instead of the above, in front of every command you wish to execute as root prepend sudo and when prompted enter your password (not the root):
          $>sudo commandname
      5. How GROMITA deals with older versions of GROMACS?
          GROMITA was originaly designed around GROMACS v.3.3.1, but it has been refined for the latest, currently, GROMACS v.4.0.4. There are minor differences in the interface of the various gromacs versions, so gromita will probably work with older versions also, although some options might require the use of the advanced mode (terminal mode)

      8. Troubleshooting

      1. Gromacs program seems to run while CPU load is very low (program halted)
      Use the interrupt button to stop execution. Select File Option ->advanced mode and try again.

      9. Acknowledgments

      GROMITA development was initially supported by a grant from NCSR "Demokritos" ("Demoerevna") and the updated version, GROMITA-4.6, was developed in the framework of "Target Identification for Disease Diagnosis and Treatment (DIAS)" project within GSRT’s KRIPIS action, funded by Greece and the European Regional Development Fund of the European Union under the O.P. Competitiveness and Entrepreneurship, NSRF 2007-2013.
      The Indicators bar on and off icons are from the "Clip Art Warehouse" (Graham Coupe http://www.clipart.co.uk/index.shtml)
      This help file was made with and OpenOffice 2.4 and is adorned with some silk icons

       

      Development Team:

      Christoforos Zarkadas, MSc & Metaxia Vlassi , PhD 

       

      Copyright © 2014-2015 PROTEIN STRUCTURE & MOLECULAR MODELING LAB,

      INSTITUTE OF BIOSCIENCES & APPLICATIONS, N.C.S.R. “DEMOKRITOS”, Ag. Paraskevi-Athens, Greece.

       

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