Hi ,
i am trying to simulate a simple rigid swnt with the one site CO2. I am starting with a specific number of molecules,big enough, and a swnt in the middle of the box. I am minimizing the problem and then i leave it to equilibrate for some time.Then i simulate it for 2 ns with a timestep of 1fs. At the begining the co2 molecules have been put in the box in a random way. After the simulation i am trying to visualize the results and i see that my nanotube has only adsorbed co2 molecules at the outside surface and not in the inner part of it which is not correct. I mean when i used a non random way to put the molecules around the nanotube i got the “right” results. My questions so are:
(a) Should i use a smaller number of molecules(now 1000) and put them closer to the nanotube ?
(b)should i increase the cutoff distance?
Jim
Dear Jim,
when you had created CO2 molecules “randomly”, did you see if all the CO2 molecules were outside the tube or some were inside well?
For an MD (non-reactive), Do you really think that outsider CO2 molecules will go inside the tube and get adsorbed there? Think about how much energy barrier the CO2 molecule would have to overcome through the CNT interface to get in from outside.
2010/5/4 Jim Jim <drazentl@…8…>
Dear Jim,
when you had created CO2 molecules "randomly", did you see if all the CO2
molecules were outside the tube or some were inside well?
For an MD (non-reactive), Do you really think that outsider CO2 molecules
will go inside the tube and get adsorbed there? Think about how much energy
barrier the CO2 molecule would have to overcome through the CNT interface to
get in from outside.
vikas,
it is not only an issue of a (potential) energy barrier. there may be
none, if the CNT
is of a large enough diameter. it is also an issue of probability: how
probable is it
for a co2 molecule to be near the opening of the CNT with the right orientation
and the right velocity vector so that it can actually enter.
cheers,
axel.
The things are: (a) There are several papers where in order to see what’s happening in a box with nanotubes and CO2 the take a number density and they put all the molecules near-but outside- the nanotubes which is not physically correct, and they saw that CO2 molecules are adsorbed both from the exterior and mainly from the interior.
(b) What i did is that i created randomly all the co2 molecules,again all outside the nanotubes just to see what will happen. And i just don’t that’s happening.
2010/5/4 Jim Jim <[email protected]...>:
The things are: (a) There are several papers where in order to see what's
happening in a box with nanotubes and CO2 the take a number density and they
put all the molecules near-but outside- the nanotubes which is not
physically correct, and they saw that CO2 molecules are adsorbed both from
the exterior and mainly from the interior.
(b) What i did is that i created randomly all the co2 molecules,again all
outside the nanotubes just to see what will happen. And i just don't that's
happening.
what i was saying is that you are looking at a "rare event" and that
even a simple geometric back of the envelope consideration
confirms this. running a single nanotube for a couple of nanoseconds
will not sample enough phase space.
this is why people do that what you describe in (a). the question is
about finding a way to quantify the bias that you apply.
there is a huge pile of research on these issues.
cheers,
axel.
So you suggest me to change it ?and put them near the nanotubes?
So you suggest me to change it ?and put them near the nanotubes?
i suggest that you first explore the statistical mechanical implications.
it is not as simple as placing the molecules where you expect them to be.
axel.
That makes sense. I thought that the CNT is periodic along axial direction (his system is p p p). In that case, molecules wont be able to enter through cylindrical hole. If it is open end terminated CNT with large enough space, then there is some probablity to CO2 to get in. But as Axel suggested, it is an rare event, so it may take while.
I read in MD books that CO2 is more likely to enter the interior of a nanotube.
Did you run as long, or with the same potential, or the same density and concentration? How many atoms do you have in your box? If the signal to noise is small you will need to run for a long time. Maybe tens to hundreds of nanoseconds.
Matt
Quoting Jim Jim <[email protected]...>:
I had a box [0.0-343.913850]x[0.0-343.913850]x[0.0-343.913850] Angstrom. I put there 1000 molecules.Temp=300K and P=1atm. I tried to run for 2 ns + 100ps for equilibration and minimization. The results that i read from the paper are with these numbers but unfortunately my co2 molecules are not adsorbed inside.
how long is your CNT?
2010/5/4 Jim Jim <drazentl@…8…>
i tried it for 100-150 nm