I am using packmol to create a initial configuration for my simulation run in order to create a stable system.
I am using this command in gromacs to create the initial configuration
gmx editconf -f input.pdb -box 2.5 2.5 2.5 -o output.gro
( had specified 25A box length in packmol )
The problem is that the output configuration file has different location of molecules when compared with the initial configuration generated by packmol. It seems gromacs is again randomly distributing the molecules inside the box.
This wasn’t the case if you use genbox command in older version ( as mentioned in some online tutorials). Should I be adding something to this command?
An easier workaround is to not to specify the box and just run gmx editconf -f input.pdb -o output.gro and then manually add the box length in the output file at the bottom.
gmx editconf will not rearrange the molecules, as you have told it to do nothing. It may “move” some molecules across the PBC, but their coordinates/location within the infinite PBC system will be identical.
Why are you running the coordinate file through editconf to generate another coordinate file which has nothing changed? What are you actually wanting to do by using this script?
It doesn’t have to be in .gro, any coordinate file format will work, including .pdb. As noted on in the gmx help grompp and all the other gmx scripts, they will all take any of the listed coordinate file types.