weria-pezeshkian / freedts

a package to simulate biomembranes at mesoscale

FreeDTS is software to perform computational research on biomembranes at messocpic length-scale. In FreeDTS, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included into the software that allow for simulation of framed membrane with constant tension, vesicles with various fixed volume or constant pressure difference, confined membranes into the fixed region of the space, constant fixed global curvature and application for external forces on regions of the membrane. In addition, the software allows one to turn off the shape evolution of the membrane and only explore inclusions organization. This allows to take realistic membrane shapes obtained from Cryo-ET and obtain heterogeneous organization of biomolecules which can be backmapped to finer simulations models.

Important Notes

Please always download the latest version as some cosmetic changes will be done until the final release of this version

Getting started with FreeDTS

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About FreeDTS
Download & Install
Citations
User Manual
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Source code map

version 1.0

See also: Weria Pezeshkian, John H. Ipsen; Mesoscale simulation of biomembranes with FreeDTS Nature Communications 15 548(2024)

Developer and Contribution

Weria Pezeshkian ([email protected]; [email protected]), Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, DENMARK

Copyrights: It is available under a CC-BY-NC-ND 4.0 International license

freedts's Issues

Can I put the protein on the two side of the membrane?

Hi, my aim is to place the curvature protein on the two side of the membrane, does it possible to use FreeDTS to do that ?and how can i change the inclusion parameter to do that?

Thank you very much

windows compilation

For anyone interested I was able to compile on windows easily :

add #include in vertex.cpp and CNTCell.cpp

change line 29 in Job.cpp by

else if (Exe.size()>3 && (Exe.at(Exe.size()-4)!='/' && Exe.at(Exe.size()-4)!='\' ))

windows use "" so when executing it looks like ......\DTS -in input_2.dts -top top.top

cd dts_src
cl /O2 /EHsc *.cpp
cl /FeDTS *.obj
move DTS.exe ...

cd ..
cd dts_convert
cl /O2 /EHsc *.cpp
cl /FeCNV *.obj
move CNV.exe ...

cd ..
cd dts_generate
cl /O2 /EHsc *.cpp
cl /FeGEN *.obj
move GEN ...
cd ..