Hi users,
I need to simulate DMSO united atom model with four interaction sites, O,S,C and C.
In the force field paper, it was given to constraint the internal degrees of freedom using SHAKE algorithm.
but when I was using SHAKE to constraint two bond_types and two angle_types , bonds are being constrained but not angles…
can we fix it???
IS there any way to overcome this problem.
thanks in advance…
karthik kumar
I don't know if this helps, but here are the commands I've been using
to successfully equilibrate a system of water constrained using shake.
Compare them with what you are using:
fix fshake all shake 0.0001 10 100 b 1 1
fix fnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 25000.0
The "1 1" refers to the bond type and angle type numbers associated
with the O-H bond and the H-O-H angle.
(Comments: I have not optimized these parameters. For one thing, it
looks like I made the Pdamp value too large, and you probably want to
use iso, not aniso. For the second command, try this instead:
fix fnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0)
Good luck.
Andrew
(P.S. I have not had much success using shake on molecules much larger
than this.)
I don't know if this helps, but here are the commands I've been using
to successfully equilibrate a system of water constrained using shake.
Compare them with what you are using:fix fshake all shake 0.0001 10 100 b 1 1
Correction, that should have been:
fix fshake all shake 0.0001 10 100 b 1 a 1
fix fnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 25000.0
The "1 1" refers to the bond type and angle type numbers associated
with the O-H bond and the H-O-H angle.
Correction: It should say:
The "b 1 a 1" refers to the bond type and angle type numbers
associated with the O-H bond and the H-O-H angle.
2. I even tried to overcome by using RIGID, but couldnt use NPT with rigid.
Why not? I think this works.
Steve
Hi steve Sir,
you mean to say rigid/NPT has been implemented in LAMMPS package. if so can you please give the details, since i couldnt find it in manual
Thanks
karthik kumar
No, I meant that you should be able to use fix npt and fix rigid
together, since fix rigid contributes to the virial (pressure) of the system.
But you need to make sure that you don't integrate the particles
in the rigid bodies twice, since both fixes will do that by default.
With fix npt you can exclude some or all of the particles
from the time integration portion, so you should exclude the rigid
body atoms and let those be integrated by fix rigid.
I think that will work, so please give it a try and let us know.
Steve