One of the biggest issues you face when you first start doing molecular dynamics (MD) simulations is how to create an initial geometry that won’t blow up in the first few time steps. Repulsive forces are very steep if the atoms are too close to each other, and if you are trying to simulate a condensed phase (liquid, solid, or interfacial) system, it can be hard to know how to make a sensible initial structure.
Packmol is a cool program that appears to solve this problem. It 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. It works with PDB and XYZ files and appears to be available under the GPL. Very, very cool!
Packmol,
I agree.. I used Packmol to work with GROMACS on surfactant solutions. That worked great. Without Packmol, very rarely I could start with a initial geometries for these kind of systems
Really a OUTSTANDING tool!
Makes really simple to build rather complex simulation boxes, and it works smoothly most of the time.
The feature I found missing is a tool to fill the box with solvent without having to calculate the number of solvent molecules in advance. If the program had a script command to simple input the desired density and the solvent_pdb_file_name, to instruct the program to fill up the empty space with such solvent at the requested density, then it would be PERFECT. Yet many tools to fill up boxes with common solvents are available, so you may simply build your system without solvent and filling it up later with a different program.
i’ve already installed packmol and downloaded the examples files. But i can not run packmol, even examples files. By the way, i use ubuntu OS. I opened packmol on terminal, then the examples files. I tried this command “packmol < packmol.inp" and also "./packmol < packmol.inp". That didn't work. I tried different input file names instead of packmol which is in " ..packmol.inp". and in differents files which is in main packmol files. Please help me, this is very important to me. My e-mail adress is kemal.ege.fizik@gmail.com.
Kemal,
There are some good compilation and installation tips here: http://www.ime.unicamp.br/~martinez/packmol/quickguide/index.html#comp
But if you are still having problems, you might want to contact Leandro Martinez. The contact information for Leandro can be found here: http://www.ime.unicamp.br/~martinez/packmol/email.html