It seems, if I dump the coordinates, the molecules are not in order
(not 1.2.3.4... etc), same is true with write_restart bin file!! Does
it mean, the molecules are rearranged and got new ordering? Because of
bonded chains, ordering is important to know where the chains are. I
have wrote a code to create the ordering, but don't know whether the
monomers of a chain is also misplaced then I have to modify it to find
out monomers in order too !! Like, if I have 100 monomer single chain
disordered dump data file, does rearranging them from 1 to 100 create
the correct ordering of bonded monomers?
Monojoy:
This has been addressed on the list before. It’s faster to just dump atom positions out in the order they’re received by the master node, rather than sorting them. However, the atom numbers are the same as their original assignments, so if you’ve retained the topological information from your data file, you can recover the correct ordering and relative positions.
–AEI
Thanks Ahmed,
I am dumping the atoms they are received by master node. Used a
fortran code to sort them. When I use the "ascii sorted data file"
with all the velocities and bonds info and the same input file, it
does not work giving error: "Bond atoms %d %d missing on proc %d at
step N" which implies that the atoms are too far away or may be they
are missing on that particular proc. However, it works fine when I use
just the restart bin file!! This may suggest that my code is not doing
the right thing, which is not true as I checked the original data file
and sorted data file carefully.
Any help?
Monojoy
the molecules are not in order
If you have a molecular system, then each
atom in the dump file will have an atom ID and
a molecule ID. Not sure which you are talking
about. The dump doc page explains about how
atoms are ordered (or not ordered) in a dump file.
There is a also a dump_modify sort option if
you want to sort the order on some quantity,
like atom ID.
Steve
Thanks Steve! It's a molecular system and I was implying atom ID. I
was concerned whether atom IDs change while dumping the file or
writing a restart bin file as they were not arranged in order? Ahmed
answered saying that it does not which is an important thing for
sorting them in order because of the bonds. I can sort them with my
code, but seems to have problem. Might be I am not correctly doing the
sorting in the code, let me check that first!!
Monojoy
Hi Steve,
It's working now. The problem was I forgot to fold the coordinates
back to the simulation box.
Monojoy