[gmx-users] Energy conservation of crystal surface

Janne Hirvi janne.hirvi at joensuu.fi
Fri May 4 10:58:14 CEST 2007

Hello gmx-users!

Sorry that I am bothering you all the time with energy conservation issues but
this time I have problems with a crystal surface consisting of infinite polymer

I think that simulation and interaction parameters employed should be
the total energy: time step of 0.5fs, PME with a slab correction for Coulombic
interactions (f-spacing=0.1, pme-order=6, ewald-rtol=1E-8), a plain cut-off or
switch function for LJ interactions (neighborlist updated on every time step
for test purposes), and double precision. At least there hasn't been such
problems with these parameters (excluding pure LJ cut-off) earlier with other
systems. New features in this system for me are positions restraints which are
used for some atoms (160 of 46080 atoms) to maintain "original crystal shape"
and option pbc=full due to the infinite chains.  

Could it be that position restraints or full periodic boundary conditions are
responsible for the energy drift or should I just still try to equilibriate
system more in NVT ensemble? I guess that this could be the problem, because
there seems to be also some huge problems depending on number of processors
used for the simulation. Simulation with 2 processors progresses normally
although energy drift is observed, but with 4 processors simulation terminates
pretty soon and huge momentary increases in energy in intervals of 0.05ps can
be observed earlier.  

Thanks for any help,


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