I’m having an issue currently where I cannot apply fix SHAKE to water molecules in an nve/limit simulation to minimize systems. If I’m using pair_style lj/charmm/coul/long I won’t get any steps as it crashes instantly (Out of range atoms - cannot compute PPPM), however if I use lj/charmm/coul/charmm I can get a few steps in before it crashes. My SHAKE stats are the following:
It is always a good idea to relax and equilibrate your system before
starting a simulation. If disabling "fix shake" helps you do this,
People often use the "minimize" command as a first step towards
equilbrating the system. Here's an example of a mixture of tip3p
# --- atom definitions ---
# --- settings: ---
group tip3p type 1 2
fix fShake tip3p shake 0.0001 10 100 b 1 a 1
# You may have to change the atom, bond, and angle type numbers
# depending on your system. (Here I assume they are all "1" and "2").
I don’t think you can use fix nve/limit with fix shake (which we should document
as a restriction on the fix nve/limit doc page).
The reason is that fix shake is adjusting forces based on the assumption
that the next time step will move atoms to a particular position. It is correcting
the forces so the new positions will end up satisfying the SHAKE constraints.
But nve/limit is chaning the timestep so atoms won’t move to where fix shake
thought they would.
Axel’s suggestion is much better - don’t apply SHAKE until your system