https://github.com/yesint/encurv

Tools for maintaining predefined membrane curvature in MD simulations
https://github.com/yesint/encurv

Last synced: 19 days ago
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Tools for maintaining predefined membrane curvature in MD simulations

• Host: GitHub
• URL: https://github.com/yesint/encurv
• Owner: yesint
• License: gpl-3.0
• Created: 2019-07-30T13:52:35.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2023-11-11T18:16:05.000Z (about 1 year ago)
• Last Synced: 2023-11-11T19:24:35.052Z (about 1 year ago)
• Language: C++
• Size: 10.5 MB
• Stars: 2
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • License: LICENSE

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README

        
EnCurv method for maintaining membrane curvature in MD simulations.

(c) Semen Yesylevskyy, 2020. [email protected]

The method is described here:

http://dx.doi.org/10.1021/acs.jctc.0c00800

Please always cite this article when using EnCurv.

How to install:

---------------

1) Get PLUMED source code (https://github.com/plumed/plumed2)

2) Copy *.cpp files to /src/colvar

3) Compile and install PLUMED as usual 

   (see https://www.plumed.org/doc-v2.5/user-doc/html/_installation.html)

   

How to run:

-----------

Directories "example_AA" and "example_CG" contain full working examples for 

Gromacs using CHARMM36 and MARTINI force fields respectively 

These are pre-equilibrated DOPC bicelle.

Gromacs have to be compiled accordingly with PLUMED support (see Plumed docs). 

The file plumed.dat contains all parameters related to EnCurv.

To run an example:

1) gmx grompp -f md.mdp -p -c start_structure.gro -n

2) gmx mdrun -plumed plumed.dat