I’d like to fix some atoms positions during NVT simulation though all the forces are calculated including those of interaction concerned with fixed atoms.
Total number of atoms is about 448 and 3~4 atoms of them will be fixed.
I used following commands for it.
group mobile id != 3 != 67 != 123
timestep 0.0002
velocity mobile create 298. 1234567 dist gaussian
fix 1 mobile temp/berendsen 298. 298. 0.01
fix 2 mobile nve
But traj.xyz (every 2000 steps0 showed most atoms does’nt move at all even after 1,000,000 steps of integration.
Is there any wrong point in it?
If so, would you let me know of it, please?
Best regards,
Luke
2010/9/19 JhonY. I. <[email protected]...>:
I'd like to fix some atoms positions during NVT simulation though all the
forces are calculated including those of interaction concerned with fixed
atoms.
Total number of atoms is about 448 and 3~4 atoms of them will be fixed.
I used following commands for it.
group mobile id != 3 != 67 != 123
timestep 0.0002
velocity mobile create 298. 1234567 dist gaussian
fix 1 mobile temp/berendsen 298. 298. 0.01
fix 2 mobile nve
But traj.xyz (every 2000 steps0 showed most atoms does'nt move at all even
after 1,000,000 steps of integration.
no need to run that long. all you need is to run for a few steps
and create a custom dump with coordinates and velocities.
Is there any wrong point in it?
your group definition looks unusual.
have a closer look at the log file. it should
print how many atoms are in this group
due your definition.
i would have done the following:
group fixed id 3 67 123
group mobile subtract all fixed
cheers,
axel.