[lammps-users] shaking C-H bonds


My understanding is that the bonds involving H-atoms could have very high frequency and so preferably shaked to allow timestep of 1 fs………when try to use this shake command, first of all it leads to very highly negative starting pressure after minimization(shake is off during minimization) and then from 10-20 steps onwards all thermo outputs become nan………I am not sure what’s occurring…I have attached log fiel herewith…….



log.trialshake (34.4 KB)

Sounds like you are starting from a bad state, or
not SHAKEing what you expect. See the bench/in.rhodo
file - it does a SHAKE on water as well as all bonds with
H I believe. You should look carefully at the output of
the SHAKE setup and verify that the counts it produces
are what you expect.