I like to minimize a five chains in my simulation.
However, I found it is able to run with single CPU, but it can’t run under multi-CPU.
I like to modify this modeling to be able to run under multi-CPU, what can i do?
Enclosed please find the data file,input file, output file, and log file.
Thanks in advance.
1.out (3.29 KB)
data.1 (9.29 KB)
in.1 (473 Bytes)
log (797 Bytes)
It has nothing to do with your model. It is sth related to how you build up the lammps with MPI version. Read the document, especially " how to build lammps " section. Or find a local parallel computing expert to help you out.
The lammps i used was compiled by the expert of super computer center in my university.
I also asked some friend ran the job on their computer, and it was not work.
I tested your system. Actually the one cpu minimization can run (but
no warrant to be correct) and the multiple cpus minimization cannot
run with the error:
ERROR on proc 1: Bond atoms 37 45 missing on proc 1 at step 0
ERROR on proc 2: Bond atoms 21 29 missing on proc 2 at step 0
I checked you data.1 file and found the coordinates of atoms 37 and 45
are as follows:
-15.9473 -20.6692 8.4152
-8.4382 -4.6255 -16.7348
The distance between these two atoms is ~18 angstroms (considering the
pbc), which is far from the bond length r0=1.5 angstrom in your in.1
file. I also viewed your system with vmd and found the structure is
So please check the initial structure first and do lammps simulation
with reasonable initial configuration!!!
Thanks so much for your kindly reply and suggestions.
I will rewrite the initial configuration and test it again.