I have one equlibrated PIM polymer data file & solvent water data files. I would like to combine both data files together & for that I designed the water block so that it could have 10 angstrom gap from the polymer membrane. After that, I tried with read data command using add apppend offset of lammps. However, the job was aborted every time with that. I also tried with vmd as I have both psf & pdb file but the merge tools in vmd don't have the parameter for polymer so it also didn't work. Could anyone please suggest any external tool that might help to resolve the issue of merging?
What kind of error do you get when you try to do this in LAMMPS? Are you sure you need the offset keyword, rather than shift, if you are trying to make a gap between the polymer and the solvent?
Otherwise, you could try merging them in Ovito https://www.ovito.org/ . It can read LAMMPS data files as well as .pbd, .xyz, and many others (not sure about .psf though).
Jyri Kimari Thanks for your answer. I have designed the water molecules so that it have a gap with the polymer. So for that , I didn't use shift keyword. I used the append because the polymer & water both have duplicate types.However, I don't think this method would work as I equlibrated the polymer previously & the image flag in the data file might not be zero.
I have tried OVITO. However, it couldn't add the angles and bonds of water probaly because it mixes up with the same type name of polymer.
I have tried VMD but it loads the unwrap coordinates of the polymer. If I wrap that in VMD it would breaks the bonds ( got this error: bond/angle/dihedral extent > half of periodic box length)
Is there any easy way by that I can merge this two file?
- Badges
- Science topic