[gmx-users] using packmol in Gromacs 3

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 22 14:06:02 CET 2009

John Bennett wrote:
> Dear Gromacs Users,
> I created a starting structure that includes 100 n-dodecane molecules ( 
> pdb file ) using packmol. And I want to use the packmol pdb file in 
> Gromacs 3.3 . Can I directly start generating Gromacs top and crd file 
> with using pdb2gmx ? For example to use a packmol pdb file in Amber it 

As long as you have a suitable topology, you do not need to use pdb2gmx (which 
probably doesn't have an entry for n-dodecane in any of the force fields, anyway).

> is necessary to add TER cards betwen each seperate molecule. Are there 
> anything like that I must do for using packmol pdb file in Gromacs ? And 
> units in packmol pdb file is angstrom . So Should I convert units to nm 

Gromacs can use .pdb files as input.

> ? Finally What is the latest stable version of Gromacs ? I think Gromacs 
> 4.0.3 is still a beta version ?

Version 4.0.4 is the latest stable version (4.0.3 was not a beta, either).


> Thanks in advance!
> Regards
> ------------------------------------------------------------------------
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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