[gmx-users] umbrella histograms

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Aug 13 17:37:22 CEST 2010

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


-- 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)


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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