Depending on your system and chosen thermostat, gen-vel=no can be a
dangerous idea (very small original velocities simply get scaled up);
besides, you should be able to equilibrate from a gen-vel=yes pretty
quickly. I don't disagree with Justin's comment, but just because it
works doesn't mean its what you should do. I'd stick to an established
procedure.
Chris.
-- original mesage --
Hi Justin
I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)
Cheers
Gavin
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