Hi All:
what we can do if we need to use both energy minimization and fix shake?
Thanks,
Fatemeh
Hi All:
what we can do if we need to use both energy minimization or minimize command and also fix shake command?
Thanks,
Fatemeh
you can massively increase the force constants of the bonds or angles
that you want to keep constrained. axel.
Thank you Axel. from your reply, I understand that I can remove fix shake command so can use minimize command . instead, I should increase the force constants ( in my case, the constant of K for fene bond style potential). I will check this and inform you about the result.
Fateme
Thank you Axel. from your reply, I understand that I can remove fix shake
command so can use minimize command . instead, I should increase the force
constants ( in my case, the constant of K for fene bond style potential). I
will check this and inform you about the result.
yes, for minimization, it doesn't matter how strong the bonds are,
since you are not doing MD and are looking to keep the distance
at the R0 value instead.
i would probably also replace the fene potential with a harmonic potential.
cheers,
axel.
You can't do this in LAMMPS (I don't even know
how to formulate that as an easy-to-solve minimization
problem).
But if you are only using minimization as a pre-equiibration
step for MD, you don't need to do this. If the bond lengths
are a little off when you start dyamics, SHAKE will rapidly
correct them (e.g. on the first step).
Steve
Steve and AXel:
I removed minimize command and as you said fix shake could rapidly correct my bonds, however, the results for energy and temperature are strangely high!
I assumed that at first I need to relax my system. Therefore, I removed fix shake (before MD) and tried first to relax the configuration of particles using minimize!
I used the style hftn for minimization and still my fene bonds are too long!
I appreciate any advice or comment as I really do not know what to do next! Can the choosing the style of minimization be important?
Thanks,
Fateme
If you're saying that after running dynamics for a while, your energies
are still too high, then energy minimization will do nothing to help that.
It might mean that your system (polymer chains?) is simply poorly
equilibrarted, and there's not much you can do besides build it
smarter or run longer. If these are simple linear FENE bead/spring
chains you can look at fix bond/swap which is Monte Carlo-based
relaxation procedure.
Steve
Thanks Steve. No, my system is not a polymer chain. It includes two types of atoms. I am using LJ potential for all pair interactions and FENE only for one type of atoms( the heavier atoms) . Can I use fix bond/swap or it is only for polymer chains?
F.
before jumping from one guesstimated hypothesis to another,
why don't you produce a small(!) example that illustrates your
problem. it is often much easier to discuss an object when one
can see how it behaves.
also, if you follow the list for a while, then you may notice
that problems are not often happening, where people initially
assume them to be. again, this can only be resolved by
having a simple, easy to run, and complete example.
cheers,
axel.
I don't know - I suggest you read the doc page.
Steve