Hello Alex,
The first error I have faced in this simulation is the error “Out of range atoms - cannot compute PPPM” and that’s the reason for the high value of neighbor list. By increasing this it ran for a longer time but stopped before reaching the desired temperature.
I used NPT because the pressure is fixed at a particular temperature for the vapor phase to exist. I also tried it with NVT but it also gave me the same error. I have also tried reducing the time, increasing the frequency of creating neighbors etc.
The visualization only shows the compression of my simulation box until the error shows up.
Thanks for the help.
Rahul
Hello Alex,
The first error I have faced in this simulation is the error "Out of range
atoms - cannot compute PPPM" and that's the reason for the high value of
neighbor list. By increasing this it ran for a longer time but stopped
before reaching the desired temperature.
which means that you have only cured the symptom and not the cause.
I used NPT because the pressure is fixed at a particular temperature for the
that statement makes no sense. you can either choose the density or
the pressure to be maintained, but not both (unless you use a much
more complex thermodynamic ensemble).
vapor phase to exist. I also tried it with NVT but it also gave me the same
which means that an NPT integrator doesn't solve the problem. so why
use the more complex and less easy to calibrate integrator over the
simple one.
error. I have also tried reducing the time, increasing the frequency of
creating neighbors etc.
as usual, this sounds like you should *first* check your simulation
parameters and initial configuration without a thermostat and see, if
you can properly conserve energy. then you need to find a simple way
to quickly and reliably reproduce the situation that causes the error
and then collect coordinates for that situation more frequently and
check with visualization or other measures (dump velocities/forces and
determine whether there are atoms moving very fast).
The visualization only shows the compression of my simulation box until the
error shows up.
which already tells you that NPT is wrong for your setup. but the
cause of the out-of-range error is some atom moving very fast, which
is more likely due to too large a value for the time step (as is the
fact that the error happens with increasing temperature).
in general, it seems that you are lacking practical experience in how
to properly set up MD simulations and thus need to find somebody in
your group or institute or otherwise close by, that can tutor you.
what you describe are issues that can often be resolved in a
person-to-person session, but are very time consuming and complex to
handle over e-mails (since for most problems, it is fastest to find a
solution by looking over your shoulder while you set things up).
axel.