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

PLUMED Grid Issue

10/4/2022

0 Comments

 
- Problem

I recently noted one of the systems we are simulating suffered from decreasing performance as the simulation progressed. Further investigation revealed it is not the actual performance of the simulation that was lower, but the fact that PLUMED needed increasingly large amounts of time to pre-process the HILLS file for each replica.

This is not an issue for a short-running simulation but for one where the simulation time runs into several μs (such as Coarse-grained simulations), it can completely hinder the trajectory from progressing past a certain point in time.

- Solution

Comparisons with other systems and similar issues mentioned in the issues of the PLUMED github repository, as well as in the PLUMED mailing list, pointed in the direction of a grid-related setting being the cause of the delay, specifically, the fineness/coarseness of the grid. 

The two files below (CORRECT PLUMED INPUT FILE & OLD PLUMED INPUT FILE) highlight a different way of specifying the grid density.

In the `old` file, the grid spacing was manually specified with the GRID_SPACING argument in the METAD block.

In the `correct` file, that line is absent from the file. In the absence of a GRID_SPACING or a GRID_BIN argument, PLUMED is going to use a grid spacing value equal to 1/5 of the Collective Variable (CV) width, for each CV, espectively.

Further testing is required but this value appears to be a robust default and has solved this issue in this particular instance.


CORRECT PLUMED INPUT FILE

C1: RMSD REFERENCE=rmsd_reference.pdb TYPE=OPTIMAL

COM1: CENTER ATOMS=1-122
COM2: CENTER ATOMS=123-244

D1: DISTANCE ATOMS=COM1,COM2

METAD ...
ARG=C1,D1
SIGMA=0.4,0.8
HEIGHT=0.005
PACE=100
LABEL=meta
BIASFACTOR=2.0
TEMP=300
GRID_MIN=0,1
GRID_MAX=4.5,6
... METAD
UPPER_WALLS ARG=C1 AT=4 KAPPA=300.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall
UPPER_WALLS ARG=D1 AT=5.5 KAPPA=300.0 EXP=2 EPS=1 OFFSET=0 LABEL=u2wall

# monitor the two variables and the metadynamics bias potential
PRINT STRIDE=10000 ARG=C1,D1,meta.bias FILE=COLVAR
​


OLD INPUT PLUMED FILE (do not use!)

C1: RMSD REFERENCE=rmsd_reference.pdb TYPE=OPTIMAL

COM1: CENTER ATOMS=1-122
COM2: CENTER ATOMS=123-244

D1: DISTANCE ATOMS=COM1,COM2

METAD ...
ARG=C1,D1
SIGMA=0.4,0.8
HEIGHT=0.005
PACE=100
LABEL=meta
BIASFACTOR=2.0
TEMP=300
GRID_MIN=0,1
GRID_MAX=4.5,6
GRID_SPACING=0.01,0.01
... METAD
UPPER_WALLS ARG=C1 AT=4 KAPPA=300.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall
UPPER_WALLS ARG=D1 AT=5.5 KAPPA=300.0 EXP=2 EPS=1 OFFSET=0 LABEL=u2wall

# monitor the two variables and the metadynamics bias potential
PRINT STRIDE=10000 ARG=C1,D1,meta.bias FILE=COLVAR

0 Comments



Leave a Reply.

    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.