From: Axel Kohlmeyer (
Date: Thu Sep 13 2012 - 02:23:08 CDT

On Thu, Sep 13, 2012 at 5:50 AM, Li, Yanfei <> wrote:
> Hi, VMD users,
> when i load LAMMPS trajectory file using VMD, it gave me error:
> inconsistent number of atoms.
> The format of dump file is " dump 1 all custom 1000 dump.fs01 id type x
> y z ".
> some atoms are lost during the simulation.

there is your problem. VMD cannot handle trajectories
with a varying number or type of atoms natively. you either
have to use some kind of workaround or use a different
visualization software.

> Then i cheacked the email list about such problem, and tried output
> format " dump 1 all xyz 1000 dump.fs01 ".
> But it still error: missing type or coordinate in file.

yes. for the same reason.

> Does anyone know which format in VMD will not care about "inconsistent
> atom number or missing type/corrdinate" problems? Thanks a lot!

there is no such format. there are two types of workaround:

1) create one file per frame, load each of them as separate
molecules and use the multimolanim plugin.

2) use some kind of scheme, that compensates the missing
atoms with dummy atoms, that are not shown with some method.
the topotools plugin provides one variant optimized for systems
without bonds.

but first of all, i would recommend to check, *why* you are
"losing" atoms. with a program like LAMMPS that is almost
always a sign of a simulation gone bad.


> Best,
> Yanfei

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.