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Energy Minimization

Performs energy minimization and molecular dynamics simulation of input structures.


The Energy Minimization module is accessible from the Simulate section of the main menu.

Basic Usage

The purpose of the module is to use energy minimization and molecular dynamics to remove bad contacts from biomolecular models parameterized in the CHARMM forcefield.

Users will input a reference PDB file name, along with matching starting structure (in either PDB or DCD format) and CHARMM topology (PSF) files. Four modes of operation can be chosen:

  1. minimization alone

  2. minimization followed by molecular dynamics

  3. minimization followed by molecular dynamics leading to a second round of minimization

  4. molecular simulation (energy minimization and/or molecular dynamics) with a user supplied input file.

These four options are explored in three cases below.


Screen Shots and Description of Input Fields

These examples show minimization of a single structure and a minimization and molecular dynamics run using advanced inputs from a DCD containing several structures.

Case 1: Single Structure Minimization

This example minimizes a single structure input as a PDB using the default CHARMM 27 forcefield.

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Example Output

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Files Created in Example

Case 2: Minimization and Molecular Dynamics of Multiple Structures

This example minimizes and then runs moleclar dynamics on every structure in the input DCD using the CHARMM 36 forcefield.

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When a run type of minimization/md or minimization/md/minimization are selected additional options related to the molecular dynamics simulation are revealed.

The advanced input section is accessed by ticking the "Check Box for Advanced Input".

Example Output

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Files Used and created in Example

Case 3: Advanced Usage: User Supplied Input Files

It is possible to provide an input file that allows for the simulation of more complicated systems.

This aspect is for experienced users.

When a run type of supply input file is chosen then one can select the name of the namd input file name.

The PDB, (DCD/PDB), PSF, and output file name read in from SASSIE-web take precendence for the files that may be listed in the user supplied input files. Specifically, the following input file keywords are overridden by the values provided by the userinput in SASSIE-web


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It is also possible to upload velocity and extended system files which is often required for continuuing / restarting a previous trajectory.

When a run type of supply input file is chosen and one selects the check box to enter restart files then the option to enter the filename(s) of velocity restart file and/or extended system restart file is provided.

If you check the box to enter restart files then the following keywords are overridden by the values provided by the user in SASSIE-web


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 restartname             output/

should be written as

Files Used and Created in Case 3 Example

Reference(s) and Citations

  1. Scalable molecular dynamics with NAMD James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. J. Comput. Chem. 26, 1781-1802 (2005). BIBTeX EndNote Plain Text

  2. NAMD User's Guide

  3. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger, Comp. Phys. Comm. 183, 382-389 (2012). BIBTeX EndNote Plain Text

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