Cluster Analysis on LAMMPS trajectory file

Hello,

I have a dump file generated by LAMMPS. In this file, a long chain molecules is in the environment of solvent molecules. We want to study the structure of this long chain polymer. I know that Amber or Gromacs can do cluster analysis on a trajectory file. I have read through the LAMMPS manual, but I have not found such tools. Can any one give me some hints on how to do this in LAMMPS?

Thanks.

Andy

Please have a look at compute/cluster command.

Hello,

I have a dump file generated by LAMMPS. In this file, a long chain molecules is in the environment of solvent molecules. We want to study the structure of this long chain polymer. I know that Amber or Gromacs can do cluster analysis on a trajectory file. I have read through the LAMMPS manual, but I have not found such tools. Can any one give me some hints on how to do this in LAMMPS?

what kind of "cluster analysis" are you talking about? people in
different communities use this term for different things.
so are you looking to cluster trajectory frames into frames with
similar geometrical structure? or looking for determining the size of
clusters?

mind you, that it is also possible to use gromacs' tools on
trajectories generated with LAMMPS.

axel.

I am meaning the similar geometrical structure using clustering analysis. I am not familiar with Grimaces. But I will look into their manuals to see what can I get from there. Thanks!

Hi Axel,

When you were saying the gromacs’ tool, what tool were you referring to? I have been using lammps for a while but I am not familiar with gromacs. Could you please tell me some details? Btw, I found the there is a plugin CatDcd which is a plugin in VMD that may help convert lammpstrj into trr or xtc, which are gromacs’ output types. Thanks.

Andy

BTW, this could be up there with the most un-LAMMPS question I have seen on the LAMMPS mailing list. I would probably ask that community.

Hi Axel,

When you were saying the gromacs’ tool, what tool were you referring to? I have been using lammps for a while but I am not familiar with gromacs. Could you please tell me some details? Btw, I found the there is a plugin CatDcd which is a plugin in VMD that may help convert lammpstrj into trr or xtc, which are gromacs’ output types. Thanks.

please keep in mind, that is was *you* that mentioned gromacs/amber
and remarked that they can do the kind of clustering tools you are
looking for. all i said about this is, that it *is* possible to use
the gromacs tools for LAMMPS trajectories. in fact, i have been asked
about simplifying this by other LAMMPS users and personal
collaborators of mine in personal communications and have implemented
a quasi-topology generator to my TopoTools plugin for VMD for that
purpose. that tool can generate a topology with data sufficient for
analysis tools, but not for MD simulations with gromacs from a LAMMPS
data file.

the rest is really a gromacs question and off topic for this list.
gromacs, like LAMMPS, has a documentation that is available for you to
study and learn from. if you expect that i will prepare a custom and
digested explanation for you, we will have to start discussing a
personal consulting fee.

axel.