[gmx-users] umbrella histograms

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Aug 13 17:56:52 CEST 2010

Thanks Chris

I have equilibrated the system at 600 K in a previous run therefore
would it not be equilibrated, and also would the velocities from the
final configuration of the equilibration not be sufficient as
equilibrium velocities going into the main simulation


chris.neale at utoronto.ca wrote:
> As I said before, please plot the position vs. time. It would be best
> if you can make a graph of this and post it to some web tool. I use
> photobucket, but there are many others.
> I realize that you think you are starting at equilibrium, but there
> are always things that can have unexpected consequences, not the least
> of which is:
> ref_t       = 600
> gen_vel     = no
> Chris.
> -- original message --
> Dear Chris
> In relation to the correspondence below, I should've mentioned that the
> peaks are symmetrical about the equilibrium distance as supposed to the
> there being one main peak at the equilibrium distance. Also
> should there be much of difference if you set pull_init to equal the
> distance between the COMs from the initial configuration, or if you set
> the value in the mdp file (which may be slightly different from that of
> the initial configuration). When I set pull_init to equal the that of
> the initial configuration i.e.pull_init =0 and pull_start = yes, there
> is much less fluctuation about the equilibrium distance than if I set
> pull_init to a value that is close to that of the initial configuration.
> (note all other parameters are the same)
> Gavin
> chris.neale at utoronto.ca wrote:
>> Dear Gavin:
>> plot the position vs. time. Probably you will see it sample around one
>> value, then discover a new state, and make a sharp transition to
>> another value. If the new state is much more favourable than the
>> initial state, then you can discard the initial state as
>> equilibration. It might not be though...

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