Metadyn View questionnaire

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http://metadyn.vscht.cz

How often you use MetadynView to visualize metadynamics data? *

routinely, I use mostly MetadynView

time to time, I use MetadynView as well as other tools

I have tried MetadynView

never

How do you use/prefer to use MetadynView?

online at http://metadyn.vscht.cz

online at my own web installation

offline

not interested

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Are you satisfied with MetadynView?

I’m satisfied and I’m using it

I’m satisfied but I’m used to other tools

I’m satisfied but other tools are better

I’m not satisfied with some features

I’m completely dissatisfied

don’t know

Clear selection

Are you satisfied with MetadynView documentation?

completely satisfied

completely dissatisfied

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Which other tools you use to get free energy surfaces from HILLS files?

Plumed’s sum_hills

general mathematics or statistics packages (e.g. Matlab, R etc)

a homemade tool

Other:

Which current features of MetadynView you use/are interested to use?

visualization of 2D free energy surfaces

visualization of 1D free energy surfaces

zooming in/out

matching points in the free energy surfaces with simulation snapshots

absolute bias potential / free energy measurement

free energy difference measurement

export to image

export to a matrix file (bias.txt)

Are you using MetadynView to make images for publications?

yes, I use/would use image output of the tool

yes, I use/would use a matrix output file (bias.txt) of the tool followed by finishing of image in other software

don't know

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Which features you miss in MetadynView?

visualization of 3D free energy surfaces

user setting of ranges of CVs and free energy

synchronised visualization of trajectory

numeric input of simulation time (i.e. other than slider)

choice of color scales schemes

high resolution image output

better setup of image appearance (e.g. font size)

vector image output

movie output

support of other metadynamics packages

calculation of free energy surfaces from COLVAR files from unbiased simulations

other types of calculation of free energy surfaces (e.g. on-the-fly reweighing)

Other:

Would you share your HILLS files from published simulations in a public database with visualization by MetadynView?

yes, I would like to put my HILLS files into a public database

maybe

don't know

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Do you produce or do you plan to produce in near future some extremely large HILLS files that would require use of big data tools (e.g. Hadoop or Spark) to calculate free energy surfaces?

yes, I'm producing/plan to produce extremely large HILLS files

don't know

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Would you use MetadynView as an application for mobile phones or tablet PCs?

yes, for Android

yes, for Apple

yes, for other OS

don't know

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Do you have some other suggestions, comments etc?

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