BROMOC Suite (2011-2014)

If you use this program please site us:

BROMOC Suite: Monte Carlo/Brownian dynamics suite for studies of ion permeation and DNA transport in biological and artificial pores with effective potentials. Pablo M. De Biase, Suren Markosyan, and Sergei Noskov J. Comput. Chem., 2014, published online: 15 DEC 2014, DOI: 10.1002/jcc.23799

BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores Pablo M. De Biase, Carlos J. F. Solano, Suren Markosyan, Luke Czapla, and Sergei Yu. Noskov* J Chem Theory Comput. Jul 10, 2012; 8(7): 2540-2551. Published online May 24, 2012. doi: 10.1021/ct3004244

Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials Pablo M. De Biase, Suren Markosyan and Sergei Noskov J Comput Chem. 2014 Apr 5;35(9):711-721. Article first published online: 12 FEB 2014 DOI: 10.1002/jcc.23544

Author: Pablo M. De Biase e-mail: pablodebiase@gmail.com

add to .bashrc export PATH=~/bromoc/bin:~/bromoc/tools/scripts:$PATH

ALL

To install all: inside BROMOC folder

For GNU Compilers

$ ./install

--or--

For INTEL Compilers

$ ./install intel

CG-GCMC-BD

$ cd cg-gcmc-bd/src

For GNU Compilers

$ make clean -f Makefile_gfortran $ make -f Makefile_gfortran
$ make install -f Makefile_gfortran

--or--

For INTEL Compilers

$ make clean -f Makefile_intel $ make -f Makefile_intel $ make install -f Makefile_intel

IMC-MACRO

To compile:

$ cd imc-macro/src

For GNU Compilers

$ make clean -f Makefile_gfortran $ make -f Makefile_gfortran
$ make install -f Makefile_gfortran $ cd ../scripts $ ./mklnks

--or--

For INTEL Compilers

$ make clean -f Makefile_intel $ make -f Makefile_intel $ make install -f Makefile_intel $ cd ../scripts $ ./mklnks

PB-PNP

To compile:

$ cd pb-pnp/src

For GNU Compilers

$ make clean -f Makefile_gfortran $ make -f Makefile_gfortran
$ make install -f Makefile_gfortran

--or--

For INTEL Compilers

$ make clean -f Makefile_intel $ make -f Makefile_intel $ make install -f Makefile_intel

TOOLS

To compile:

$ cd tools/src

For GNU Compilers

$ ./makeall

--or--

For INTEL Compilers

$ ./makeall intel