Dear all,
I am trying to perform an equilibration of non-periodic system (boundayr s s s) and then deform system at fixed initial density
Firstly, I generated polymer structure but density is too small = 0.004 (I cannot create structure with wished density)
Secondly, I compressed simulation box along with equilibrating system using (fix nve + fix langevin) at high temperature 500 K to target density = 0.9, e. g.
At this point, before deformed system at lower temperature 100 K, I had equilibrated system using fix nve + fix langevin and then fix nvt to downward temperature to 100 K.
Here, the problem take placed, in relaxation process volume increase so fast.
Could you please suggest me what I could do for my problem. How can I do to get target density non-periodic system.
Thanks so much for your time.
Ha.
Dear all,
I am trying to perform an equilibration of non-periodic system (boundayr s s
s) and then deform system at fixed initial density
Firstly, I generated polymer structure but density is too small = 0.004 (I
cannot create structure with wished density)
Secondly, I compressed simulation box along with equilibrating system using
(fix nve + fix langevin) at high temperature 500 K to target density = 0.9,
e. g.
At this point, before deformed system at lower temperature 100 K, I had
equilibrated system using fix nve + fix langevin and then fix nvt to
downward temperature to 100 K.
Here, the problem take placed, in relaxation process volume increase so
fast.
have you visualized the trajectory? usually what you describe
coincides with molecules "flying away".
Could you please suggest me what I could do for my problem. How can I do to
get target density non-periodic system.
well, density is an ill-defined property for an atomic
scale object. how do you define the volume for the
density? the box volume is arbitrary.
axel.
Dear Axel,
Yes, I used Ovito to visualize, it’s look like you said.
Basing on chain.f, then I expanded the box to bound all of molecules. Therefore, I cannot fix size of box
I know It’s is not a good idea to generate non-periodic system.
Thanks for your help.
Ha.
How do you compress the volume for a non-periodic
box?
Steve
Dear Axel,
Yes, I used Ovito to visualize, it's look like you said.
Basing on chain.f, then I expanded the box to bound all of molecules.
Therefore, I cannot fix size of box
I know It's is not a good idea to generate non-periodic system.
two more comments.
1) you can have a similar setup and avoid having molecules
"fly off" by using f boundaries with and reflecting walls.
2) you need some kind of confinement to enforce any specific
density. otherwise, the system will relax to its "natural" density.
axel.
Dear Steve,
As you advised before, I used fix wall/reflect + fix langevin and nve to compress non-periodic in x, y, x directions.
And as Axel recommended, I will try f f f as boundary.
Thanks.
Ha.
Dear Axel,
Special thanks for your advice.
After compresssing to desired density around 0.85 ( my initial density = 0.18),
Then, I performed equilibration using boundary f f f and fix wall/reflect as follows:
Firstly, I used fix nve + fix langevin to relax at 500 K. In this step, total energy decrease a bit.
Secondly, I used fix nvt to relax at 500 K.
Next, Continue fix nvt to relax from 500 K - 100 K
Finally : Continue relaxing at 100 K. However, in the end of this stage press, pxx, pyy, pzz values are huge.
Is there a way to relax as above steps but I can control pressure, pxx, pyy, pzz small enough. Perhaps, to achieve density = 0.85 I compressed too much.
Thanks
Ha.
Dear Axel,
Special thanks for your advice.
After compresssing to desired density around 0.85 ( my initial density = 0.18),
Then, I performed equilibration using boundary f f f and fix wall/reflect as follows:Firstly, I used fix nve + fix langevin to relax at 500 K. In this step, total energy decrease a bit.
Secondly, I used fix nvt to relax at 500 K.
Next, Continue fix nvt to relax from 500 K - 100 K
Finally : Continue relaxing at 100 K. However, in the end of this stage press, pxx, pyy, pzz values are huge.
Is there a way to relax as above steps but I can control pressure, pxx, pyy, pzz small enough. Perhaps, to achieve density = 0.85 I compressed too much.
Impossible to answer with this vague description. Could be due to a variety of reasons. Sound a lot like your adviser or a colleague with some experience in running MD.
Axel