Molecular Modeling and Drug Design
  • About us
  • Research
  • Publications
  • Members
  • Webservers
  • Calendar
  • Blog
  • Benchmarks
  • ALLODD
  • Image Gallery
  • Publicity
  • Talks

SQUEEZE-E: How to make a simulation cell based on the shape of the molecule

10/11/2013

0 Comments

 
Read below on how the authors below made a method to define a box which is based on the shape of the molecule. This should drastically recude the number of atoms and hence simulation time! i(if the rotation is constrained)

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions
b
y Tsjerk A. Wassenaar *†‡, Sjoerd de Vries ‡, Alexandre M. J. J. Bonvin ‡, and Henk Bekker §

In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent–solvent interactions. As a consequence, periodic boundary conditions are commonly used, with a simulation box chosen as small as possible, for a given minimal distance between images. Here, we describe how such a simulation cell can be set up for ensembles, taking into account a priori available or estimable information regarding conformational flexibility. Doing so ensures that any conformation present in the input ensemble will satisfy the distance criterion during the simulation. This helps avoid periodicity artifacts due to conformational changes. The method introduces three new approaches in computational geometry: (1) The first is the derivation of an optimal packing of ensembles, for which the mathematical framework is described. (2) A new method for approximating the α-hull and the contact body for single bodies and ensembles is presented, which is orders of magnitude faster than existing routines, allowing the calculation of packings of large ensembles and/or large bodies. 3. A routine is described for searching a combination of three vectors on a discretized contact body forming a reduced base for a lattice with minimal cell volume. The new algorithms reduce the time required to calculate packings of single bodies from minutes or hours to seconds. The use and efficacy of the method is demonstrated for ensembles obtained from NMR, MD simulations, and elastic network modeling. An implementation of the method has been made available online at http://haddock.chem.uu.nl/services/SQUEEZE/ and has been made available as an option for running simulations through the weNMR GRID MD server at http://haddock.science.uu.nl/enmr/services/GROMACS/main.php.
0 Comments

Benchmark studies of NAMD and GROMACS

2/11/2013

0 Comments

 
We have recently performed benchmark studies of different systems (ranging from 200,000 atoms to 600,000 atoms) with and without GPU acceleration for the programs NAMD and GROMACS.

Larger systems seem to benefit from GPU acceleration with GROMACS; NAMD did not scale well using the GPU version.
For systems ~200,000 atoms Gromacs scales well up to 112 cores.

See more here.

Zoe

0 Comments

On the implementation of the AMBER force field in NAMD and GROMACS

2/5/2013

4 Comments

 
The AMBER force field ff99SB-ILDN has been recently shown to perform best among other force fields. See paper by the Shaw group: "Systematic Validation of Protein Force Fields against Experimental Data"

However, AMBER is not free and does not scale very well on over 256 cores, which means that it is best to run the NAMD or GROMACS codes using the AMBER force field if you are running on more than 256 cores or do not have Amber.

However, you should carefully read and implement the directions in this document for use with NAMD (NOT the UIUC one), which should give you identical energies if followed carefully.

For use with GROMACS follow these instructions: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx or http://chemistry.csulb.edu/ffamber/

Zoe


4 Comments

Analysis of MD simulations using GROMACS tools

11/7/2012

5 Comments

 
I just came across this presentation which very nicely summarises the most important analysis tools for proteins available in Gromacs:  Definitely worth reading and very good as a reference for experienced gromacs users.

Analysis tools that you can find in the presentation include:
- Looking at your trajectory
- Groups in analysis
- Root mean square deviations and fluctuations
- Radius of gyration and distances
- Hydrogen bonds
- Secondary structure analysis
- Free energy surfaces
- Principal component analysis: using Cartesian coordinates or dihedral angles
- Clustering

Evi


5 Comments

    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

    lab group members!

    Enter your email address:

    Delivered by FeedBurner

    Click to set custom HTML

    Archives

    October 2022
    December 2021
    August 2021
    July 2021
    December 2020
    November 2020
    September 2020
    August 2020
    April 2019
    September 2018
    March 2018
    January 2018
    August 2017
    February 2017
    November 2016
    July 2016
    June 2016
    January 2016
    October 2015
    May 2015
    April 2015
    January 2015
    October 2014
    September 2014
    August 2014
    June 2014
    May 2014
    April 2014
    March 2014
    February 2014
    January 2014
    December 2013
    November 2013
    October 2013
    September 2013
    August 2013
    July 2013
    June 2013
    May 2013
    April 2013
    March 2013
    February 2013
    January 2013
    December 2012
    November 2012
    October 2012
    September 2012
    August 2012
    July 2012
    May 2012
    April 2012
    March 2012
    January 2012
    October 2011

    Categories

    All
    64 Bit
    64-bit
    Academia
    Acrobat Reader
    Acroread
    Binding Sites
    Bioinformatics
    Blogging
    Career
    Chembl
    Chemdraw
    Chemistry
    Cloud Computing
    Cluster
    Compounds
    Computational Biology
    Conferences
    Courses
    Crystal Structures
    Databases
    Desktop
    Desmond
    Docking
    Drug Design
    Drug Discovery
    Education
    Email
    Excel
    Fellowships
    Ffmpeg
    Figures
    File Conversions
    Firefox
    Force Field Parameterization
    Fp7
    Free Storage Space
    Glide
    Gpu
    Grant Writing
    Gromacs
    Hpc
    Industry
    Intermolecular Interactions
    Ip Address
    Iphone
    Iso Image
    Jobs
    Library
    Linux
    Lipids
    Literature
    Maestro
    Management
    MAPS
    Materials
    Matlab
    Md Simulations
    Membrane
    Mobile Apps
    Modeling
    Namd
    Network
    Nobel Prize
    Normal Mode Analysis
    Nvidia
    Nwchem
    Off-target Effects
    Pdb
    Pdf
    Peptides
    Photoshop
    Pictures
    Plots
    Postdocs
    Presentations
    Printing
    Problem After Updates
    Programming
    Protein Preparation
    Protein-protein Interactions
    Protocols
    Publishing
    Python
    References
    Review
    Rosetta
    Scheduling
    Schrodinger
    Scripting
    Sitemap
    Solubility
    Ssh
    Teaching
    Trajectory Analysis
    Ubuntu
    Van Der Waals
    Video
    Virtualbox
    Virtual Machine
    Virtual Screening
    Visualization
    Vmd
    Voice Over Ip
    Webinars
    Website
    Writing
    Xmgrace

    RSS Feed

Powered by Create your own unique website with customizable templates.