# Packmol
Packmol - Creates Initial Configurations for Molecular Dynamics Simulations
**https://m3g.github.io/packmol**
## What is Packmol
Packmol creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.
The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.
The user must provide only the coordinates of one molecule of each type, the number of molecules of each type and the spatial constraints that each type of molecule must satisfy.
The package is compatible with input files of PDB, TINKER, XYZ and MOLDY formats.
## Usage
User guide, examples, and tutorials, are available at: https://m3g.github.io/packmol
## Installation instructions
### Downloading
1. Download the `.tar.gz` or `.zip` files of the latest version from: https://github.com/m3g/packmol/releases
2. Unpack the files, for example with:
```bash
tar -xzvf packmol-20.13.0.tar.gz
```
or
```bash
unzip -xzvf packmol-20.13.0.zip
```
substituting the `20.13.0` with the correct version number.
### Using `make`
3. Go into the `packmol` directory, and compile the package (we assume `gfortran` or other compiler is available):
```bash
cd packmol
./configure [optional: path to fortran compiler]
make
```
4. An executable called `packmol` will be created in the main directory. Add that directory to your path.
### Using the Fortran Package Manager (`fpm`)
3. Install the Fortran Package Manager from: https://fpm.fortran-lang.org/en/install/index.html#install
4. Go into the `packmol` directory, and run:
```bash
fpm install --profile release
```
this will compile and send the executable somewhere in your `PATH`.
By default (on Linux systems) it will be `~/.local/bin`. Making it available
as a `packmol` command anywhere in your computer.
`fpm` will look for Fortran compilers automatically and will use `gfortran`
as default. To use another compiler modify the environment variable
`FPM_FC=compiler`, for example for `ifort`, use in bash, `export FPM_FC=ifort`.
## References
Please always cite one of the following references in publications for which Packmol was useful:
L Martinez, R Andrade, EG Birgin, JM Martinez, Packmol: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30, 2157-2164, 2009. (http://www3.interscience.wiley.com/journal/122210103/abstract)
JM Martinez, L Martinez, Packing optimization for the automated generation of complex system's initial configurations for molecular dynamics and docking. Journal of Computational Chemistry, 24, 819-825, 2003.
(http://www3.interscience.wiley.com/journal/104086246/abstract)
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Packmol-分子动力学模拟的初始配置___下载.zip
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Packmol-分子动力学模拟的初始配置___下载.zip (56个子文件)
packmol-master
configure 1KB
CMakeLists.txt 1KB
.github
workflows
actions.yml 1KB
Makefile 7KB
src
resetboxes.f90 751B
swaptype.f90 2KB
random.f90 1KB
tobar.f90 1KB
comprest.f90 7KB
restmol.f90 2KB
strlength.f90 2KB
comparegrad.f90 3KB
flashsort.f90 2KB
setibox.f90 852B
initial.f90 19KB
swaptypemod.f90 356B
checkpoint.f90 4KB
writesuccess.f90 2KB
input.f90 2KB
flashmod.f90 449B
setsizes.f90 10KB
output.f90 26KB
gencan_ieee_signal_routines.f90 2KB
pgencan.f90 3KB
polartocart.f90 3KB
usegencan.f90 450B
computef.f90 6KB
jacobi.f90 3KB
computeg.f90 8KB
ahestetic.f90 792B
fparc.f90 2KB
sizes.f90 915B
gencan.f 198KB
gparc.f90 3KB
exit_codes.f90 511B
gwalls.f90 12KB
cenmass.f90 2KB
title.f90 495B
setijk.f90 1019B
getinp.f90 38KB
compute_data.f90 2KB
heuristics.f90 4KB
AUTHORS 471B
app
packmol.f90 30KB
solvate.tcl 129KB
LICENSE 1KB
testing
water_box.inp 155B
ieee_signaling.inp 527B
water.pdb 255B
ieee_signaling.pdb 109B
header 142B
compile_cmake.sh 646B
.gitignore 129B
release.sh 1KB
fpm.toml 368B
README.md 3KB
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