Hi vishnu.
I am presuming that while running the original simulation there were no problems.
Are you using single processors or multiple processors while rerunning the simulation with the dcd file.
If you are using multiple processors, can you try using single processor and see if the problem still persists.
I am also assuming that you are using the same potential while rerunning the simulation.
Thanks
Arun.
Hi Arun
There was no problems during the original simulation.
Regarding processors, i tried using single processor in a parallel lammps and also i tried running the case using serial lammps.
None of these seems to be helping.
ADDITIONAL INFO: There has been a warning during the rerun: Inconsistent image flags.
Thanks in advance
Vishnu Prasad K
Hi Arun
There was no problems during the original simulation.
Regarding processors, i tried using single processor in a parallel lammps
and also i tried running the case using serial lammps.
None of these seems to be helping.
ADDITIONAL INFO: There has been a warning during the rerun: Inconsistent
image flags.
yes, and that is the most important hint. a typical dcd format trajectory
file will write wrapped coordinates (i.e. fold all coordinates back into
the principal simulation cell) and does not contain the image flags
required to unwrap positions.
however, that will "break" molecules, that have bonds crossing periodic
boundaries and that in turn will cause all kinds of trouble, e.g. the
location of the point M of the TIP4P model is reconstructed from the oxygen
and hydrogen atom positions in the wrong location.
so before you can use this trajectory for "rerun", you have to "unwrap" it.
or start over and regenerate it as an unwrapped trajectory.
or you could write in native LAMMPS trajectory format, and either use
unwrapped coordinates or include image flags.
axel.
Hi Axel, Arun,
The problem was with the wrapped coordinates in dcds as Axel mentioned. I tried the same using native lammps trajectory with image flags, and it was working fine.
Thanking You
Vishnu Prasad K
Hi all,
This is a bit embarrassing to be reopening this issue. I assumed the issue to be well settled based on simulations on a local workstation. However, when I used the same Lammps scripts for generating and rerunning the DCD files in a cluster (super computer), the error reappeared with four point water models.
ERROR: Out of range atoms-cannot compute pppm.
I tried both unwrapped DCD file format and native .lammpstrj formats, but seems to be of no help. However both of these were woking fine on the local machine when tested.
The Lammps used in local machine and the cluster were the same version. The cluster machine did not have the user-molfile package installed during trajectory generation. The number of processors used in both cases was different.
Thanking You
Vishnu Prasad K