velocities are not taken from the .gro as far as I know. You can get
them from the .trr if you also use a .edr.
If you want to check, then do a run for only 1 ps and save your .edr
every timestep. Then run g_energy and look at the temperature.
I am not sure that a constant energy simulation in vacuum is a good
idea. When I say the initial forces become the initial velocities, I
mean this: you start with no thermal noise, your system is momentarily
at zero kinetic energy. After the first time step, you get some
velocities from the initial forces. It is quite likely that these will
be concerted motions more than random oscillations, especially if you
are using the pull code. But the kinetic energies are still quite
small, so your thermostat scales them up massively and you get a
"flying ice cube" problem (again, read about this please).
I think that you will get farther if you try to test some of these
yourself: e.g. if you think that you get initial velocities, then
think of a way to test if you really do (here you have the method I
suggested above, but it's just an analogy).
Chris.
-- original message --
Thanks for all your help. I am actually considering removing the
thermostat all together seeing as my system is quite small.
I have also started using gen_vel = yes (no matter how much I think my
system is in equilibrium). One quick question (perhaps its silly). When
you say the initial forces become the initial velocities; I thought the
initial velocities were taken from the velocities in the initial
configuration (taking into account that I do have velocities in the
initial configurations from previous simulations).
Cheers
Gavin
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