Dear all,
I have been trying to do a simulation of molecules (hexadecane) inserted
into a domain for depositing them onto a substrate.
I am using fix deposit + molecule command to get this done. Initially
there is only one molecule in the simulation box and then new molecules
are inserted within a region. For building the molecule template I have
just copy all the sections from the data file which has the info of
initial molecule and pasted into the new file (hexadecane.mol). The file
format seems to be correct and the molecule is inserted correctly. What
is wrong is that the force field I am using (opls), seems to be not
working correctly when the molecule is added and the simulation blows up
with the well known evil message:
"Bond atoms 2940 2941 missing on proc 6 at step 153". If I print the
forces, they are really big on the inserted molecule (~10^3).
So for checking, I am only running one step to let the insertion of the
first molecule be along with the preexistent one. Then I minimize the
system to avoid the blow up due to integration but to see how the
structures evolve. If I check the system.xyz.out with jmol I observe
during minimization how the potential acting in the inserted and in the
already present molecule is behaving differently. I am out of ideas now
and I have checked several times the molecule file without finding any
apparent errors. Since I just copied all the data from the data file
into the molecule file it has to be something on how the force field is
being applied to the inserted molecule (probably a bug???).
I have attached the files for the simulation so anyone can have a try.
Thanks for your time.
Regards,
Eduardo
files.tar.gz (9.45 KB)