I'm sorry 
W dniu 2015-01-20 o 18:21, Axel Kohlmeyer pisze:
I'm sorry
W dniu 2015-01-20 o 18:21, Axel Kohlmeyer pisze:please always reply to the mailing list and not individual people. thanks.
1. Yes, I know what reax is. So then, is there any smart way to create mass
spectrum of particles in the system at a specific time step or at the end of
simulation?
i don't understand this question. and i don't understand the relation
to your original question.
are you saying that you want to use an MD simulation to calculate what
would be the output of a mass spectrometer?
do you have any publication that describes the procedure for that? or
do you mean something else?
if the latter, can you please reformulate and explain a bit more?
axel.
Let me explain:
The target which I want to achieve is a chemical composition of my sample, which actually corresponds to the output of the mass spectrometer. In my previous work I was using simplified procedure, where having the potential curve I could predict "stable" chemical (mostly covalent) bonds of chosen pair of atoms based on the distances between them. That method was working quite well when I had only carbon and hydrogen in the system.
Now, I wanted to create similar procedure for the sample where interactions are described by ReaxFF.
However, now I see that it might be much more complex than I expected. So that is why I raise second question about mass spectrum.
Let me reformulate my question:
Is there any (relatively) simple way to obtain the type of bonds between atoms in the system where interactions are described by ReaxFF.
Regards,
Bartlomiej
W dniu 2015-01-20 o 21:40, Axel Kohlmeyer pisze:
Let me explain:
The target which I want to achieve is a chemical composition of my
sample, which actually corresponds to the output of the mass
spectrometer. In my previous work I was using simplified procedure,
where having the potential curve I could predict "stable" chemical
(mostly covalent) bonds of chosen pair of atoms based on the distances
between them. That method was working quite well when I had only carbon
and hydrogen in the system.
Now, I wanted to create similar procedure for the sample where
interactions are described by ReaxFF.
However, now I see that it might be much more complex than I expected.
So that is why I raise second question about mass spectrum.
indeed, and there is a facet of this kind of simulation that you
should be aware of now, that might become a problem. ReaxFF requires
the use of charge equilibration, which in turn has limitations with
charged systems (as you can see only ions in MS, you would need to
properly ionize your molecules). i am not very familiar with the
details of this, but i suggest you search the mailing list archives
for previous discussions on that subject and study the relevant
literature before you commit a lot of time on using ReaxFF for your
project only to find out that it cannot produce reliable results.
Let me reformulate my question:
Is there any (relatively) simple way to obtain the type of bonds between
atoms in the system where interactions are described by ReaxFF.
you have access to the bond order parameter through fix reax/c/species
and can dump and manually post process the data, or use fix
reax/c/bonds and collect the bond information according to the bond
order cutoff provided in the control file.(via bond_graph_cutoff).
axel.
Let me reformulate my question:
Is there any (relatively) simple way to obtain the type of bonds between
atoms in the system where interactions are described by ReaxFF.
you have access to the bond order parameter through fix reax/c/species
and can dump and manually post process the data, or use fix
reax/c/bonds and collect the bond information according to the bond
order cutoff provided in the control file.(via bond_graph_cutoff).
If fix reax/c/species doesn’t have useful info (e.g. about current
molecules which is derived from the bond-order params for each
atom), then ask Ray (CCd) further Qs about getting at the info
you want.
Steve