[gmx-users] problems with g_wham

Gavin Melaugh gmelaugh01 at qub.ac.uk
Thu Jul 8 16:02:10 CEST 2010

O.K cheers Chris. I do intend to equilibrate the system at the desired
temperature before constructing the histogram.
chris.neale at utoronto.ca wrote:
> 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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