FEMWgen : A computational tool to generate multiple windows

for free-energy calculations.

Installation

To use the code you can download using the following command:

giit clone https://github.com/groponp/FEMWgen.git 

Requirements

To run our code you need python > 3.x and the following packages:

• Optparse
• Colorama
• VMD-python last version
• Glob
• Json

conda create -n femwgen  python=3 -y 
conda activate femwgen 

Usage

#! To get help running
python FEMWgen.py --help 

#! For get usage example running
python FEMWgen.py --usage

#! it can print following
Common usage NAMD only:
-----------------------
python FEMWgen.py --psff=sistema.psf --pdbf=sistema.pdb --bin=2 --lresn="POPC POPG" --pref="resname TRP and name CH2"
--lref="resname POPC POPG and name P" --lrst="serial 38224 40079 39148 39811 20055 14892 19787 18877"
--namd="$HOME/Documents/packages/NAMD_2.14_MacOSX-x86_64-multicore/namd2" --nproc=2 --cfw=-38 --seltxt="protein" --nw=60

Common usage NAMD w/ CHARMM++:
------------------------------
python FEMWgen.py --psff=sistema.psf --pdbf=sistema.pdb --bin=2 --lresn="POPC POPG" --pref="resname TRP and name CH2"
--lref="resname POPC POPG and name P" --lrst="serial 38224 40079 39148 39811 20055 14892 19787 18877"
--namd="$HOME/Documents/packages/NAMD_2.14_MacOSX-x86_64-multicore/namd2" --nproc=2 --charm="$HOME/Documents/packages/charmrun/charmrun" --cfw=-38 --seltxt="protein" --nw=60

Restart usage:
--------------
python FEMWgen.py --restart="True" --chkpoint=FEMWgen.chkpoint --jsonfile=FEMWgen.json --cfw=-38 --seltxt="protein"

#! import module
import FEMWgenLIB

#! Setting parameters
mkw = FEMWgenLIB.MakeWindows(psff="sistema.psf", pdbf="sistema.pdb", Bin=2, lresn="POPC POPG", refprot="resname TRP and name CH2",
                   refmemb="resname POPC POPG and name P", rstmemb="serial 38224 40079 39148 39811 20055 14892 19787 18877",
                   namdPATH="$HOME/Documents/packages/NAMD_2.14_MacOSX-x86_64-multicore/namd2", nproc=2)

#! Write parameters as Json file, necesary to restart computation 
FEMWgenLIB.IO.writrJsonParms(ofile="FEMWgen.json", dic=mkw.__dict__)
mkw.__dict__

#! Running computation 
mkw.iterateWindows(cfw=-38, seltxt="protein", N=20)


#! If your computation stop for any reason continue with restart mehtod.
restart = FEMWgenLIB.RestartWindows()

#! Use checkpoint to restrart from last step
windowsOK = restart.get_NotiterateWindows("FEMWgen.chkpoint")
windowsOK

#! Running restart
restart.restart(windowsOK, cfw=-38, seltxt="protein", jsonfile="FEMWgen.json")

#! Use it into tkcosnsole into vmd or with tcl script of vmd with graphics off
source FEMWgen_v1.0b.tcl 
package require FEWgen 

#! For get help. It have all methods as python version except for restart function
FEWgen -h 

#! Return 
#!-------------------------------------------------------------------------------------------------#!
#! FEMWgen v1.0b : A Computational Tool to Generate Multiple Windows for Free-energy Calculations. #!
#! [INFO   ] usage: source FEMWgen.tcl.                                                            #!
#! [INFO   ] usage: FEMWgen -psf<PSF> -pdb<PDB> -n<N> -coj<CPJ> -bin<BIN> -lresn<LRESN>...         #!
#! [INFO   ] @uthors : Suman de Araujo A., Fernando Zonnetti and Ropón-Palacios G.                 #!
#! [INFO   ] contact to: <[email protected]>.                                               #!
#!-------------------------------------------------------------------------------------------------#!
Options:
    -psf<PSF>         File containing topology. Default 'sistema.psf'.
    -pdb<PDB>         File containing coordinates. Default 'sistema.pdb'.
    -n<N>.            Number of windows. Default 60.
    -cpj<CPJ>         Center of first windows. Default -38.
    -bin<BIN>         Spacing for each windows. Default 2.
    -lresn<LRESN>     Resname lipid component into membrane. Default 'POPC POPG'.
    -pref<PREF>       Reference atoms from protein. Default 'resname TRP and name CH2'.
    -lref<LREF>       Reference atoms from lipids. Default 'resname POPC POPG and name P'.
    -lrst<LRST>       Serial key of atoms to restraint during equilibration. Default 'serial 38224 40079 39148 39811 20055 14892 19787 18877'.
    -charm++<CHARM++> Boolean option to use o not charmrun mode with running NAMD. Default 'false'.
    -nprocs<nprocs>   Number of CPUs that will be use into energy minimization. Default 2.
    -h                Print it message.

A configs file and sample coordinates and topology could be found in the FEWgen1.0_PythonModule/configs folder.

Authors

The code was written by : Alexandre Suman de Araujo, Luiz Fernando Zonetti and Ropón-Palacios G.

Main developer: Ropón-Palacios G. [email protected]

Reference

If you want to get a theoretical framework of this code please check out our kddk article. If you use our code please cite it.

License

GPLv3