Packmol

Packmol 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!

Rating: 4.7. From 14 votes.
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13 Responses to Packmol

  1. Arun says:

    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

    Rating: 1.0. From 1 vote.
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  2. Rogelio Rodríguez-Sotres says:

    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.

    Rating: 5.0. From 1 vote.
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  3. kemal says:

    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.

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  4. Dan Gezelter says:

    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

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  5. Guedmiller Souza de Oliveira says:

    Gostaria de instalar o packmol no ubuntu, porém não consigo instalar. Depois de seguir todos os passos de instalação do site, o programa diz que foi instalado com sucesso porém não aparece para como opção no terminal do ubuntu. Se alguem souber e puder me ajudar eu agradeço

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  6. Dan Gezelter says:

    Guedmiller,

    Há alguns bons compilação e instalação dicas aqui.

    Mas se você ainda está tendo problemas, você pode querer entrar em contato com Leandro Martinez. As informações de contato Leandro pode ser encontrada aqui.

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  7. Flavia Shirata says:

    Tambem estou tentando instalar o packmol no ubuntu, mas nao entendi o que seria o “source code” que ele fala no manual, logo depois de expadir a pasta que baixei. Se alguem puder me explicar, agradeco muito!

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  8. ZEESHAN AHMED says:

    Hello
    I have installed packmol. 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.

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  9. ben says:

    how to convert the pack mol pdb file to gro file and validate it for any messing atome name or type in the topology

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  10. ernik says:

    it’s firts time i use packmol. i try to istall it in linux but i got a eror, can anyone tell me about it?

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  11. Uzoma says:

    Please I would love to know the particular OS Packmol can run on. I’ve downloaded the zipped file and extracted same. But I have no headway. I’m using Windows 8 OS. Thanks

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  12. Dan Gezelter says:

    It looks like packmol is available only as source code, so you’ll have to use a fortran compiler to build it.

    Rating: 5.0. From 1 vote.
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  13. yannick says:

    Usually I used to install and use packmol with ease. I later changed my computer and installed Ubuntu 16.04. Followed all the installation tips and even build it with gFortran , But I still get the same error. Any suggestions Please?

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