METAGUI: analyzing metadynamics simulations with VMD

[Xevi Biarnés]

Dear PLUMED users,

in regard to previous recent e-mails requesting help in the analysis of bias-exchange metadynamics simulations,

we are happy to provide you with METAGUI, a VMD plugin that allows easily analyzing metadynamics simulations generated with PLUMED (not only bias-exchange, but single replica and multiple walkers as well).

among other features, the tool allows easily:

* building-up the multidimensional free energy surface of your system under investigation, starting from the low-dimensional metadynamics biases.

* navigating through the multidimensional free energy surface: this allows exploring the 3D-structures of your molecule corresponding to each point of the free energy surface.

* identifying the kinetic attractors on the free energy surface (i.e. subdivide the free energy surface in the principal free energy wells/basins).

* checking if the number and type of collective variables is adequate to discretize your phase-space, prior to launching a metadynamics simulation.

METAGUI v2.0 is a new version of the earlier plugin which was briefly introduced in the former PLUMED tutorial held last October in Lausanne. many new features have been introduced, and errors corrected.

please, note this is an external contribution to the PLUMED software, and thus, it is not provided yet together with the PLUMED source files (maybe in new releases). However, it will soon be downloadable independently from the web-site of PLUMED.

in the meantime, we are providing you the METAGUI plugin via e-mail. the package attached to this mail contains:

- all the source files

- a README file with straightforward installation steps and simple usage.

- a manual (manual.pdf) with  details on the usage, file formats and type of calculations performed by the METAGUI plugin.

- a simulation example ready to be analyzed. if you want the trajectory files of the example to be provided to you, please, ask them to us via e-mail (they are too big to be attached to this mail).

we hope this tool will greatly facilitate the analysis of your metadynamics simulations. do not hesitate in contacting us for assistance and/or suggestions for further improvements of the plugin.

the METAGUI developers,

Xevi Biarnés

Fabio Pietrucci

Fabrizio Marinelli

Alessandro Laio

[Andrea Spitaleri]

Hi there,
this is a great job! thanks a lot. I have read the README and
manual.pdf and the cluster.in format is not discussed. just the
example.
Might suggest to add this information in the manual?

thanks a lot. great tool. I will go through.

and

2011/6/14 Xevi Biarnés <xevib...@gmail.com>:

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[ider.ron...@googlemail.com]

Hi,

I am using the cp2k to di metadynamics simulation and got only xyz files and tried to convert it xtc files (with some code I found ) in order to use METAGUI. However it did not work , so I just wanted to know if there is aa easy possibility to convert xyz files to xtc files.

Best regards

Ider

[Xevi Biarnés]

Dear Ider,

as from METAGUI 2.1, you should be able to read XYZ trajectory files directly from METAGUI. You will need to provide a structure file as well  (usually a single frame PDB or GRO file).

hope it helps,

X.

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······································································

XEVI BIARNÉS, PhD

Bioinformatics & Molecular Modelling Researcher

Laboratory of Biochemistry

Bioengineering Department

INSTITUT QUÍMIC DE SARRIÀ

UNIVERSITAT RAMON LLULL

via Augusta, 390

08017 Barcelona - SPAIN

tel: +34.93.267.20.00 ext: 418

xevi.b...@iqs.edu

xevi.b...@gmail.com

[rabeta...@gmail.com]

Dear Administrator,

I have run plane metadynamics in NAMD. I am wondering if I can use META-GUI to analyze those meta dynamics results.
Thanks.

Rabeta Yeasmin