[gmx-users] problems with g_wham

Gavin Melaugh gmelaugh01 at qub.ac.uk
Thu Jul 8 10:37:04 CEST 2010

Thanks Chris and Justin

I do get the output I want from grompp(below). The distance of 5.507 nm
is the distance that I want to start with and I assume it is therefore
the equilibrium distance for the harmonic potential. The COM distances
from the simulations fluctuate around this value which is what I want,
although my histogram is the wrong shape.

Pull group  natoms  pbc atom  distance at start     reference at t=0
       0               84        42
       1               84       126                  
5.507                 5.507



chris.neale at utoronto.ca wrote:
> I missed that pull_start = yes, sorry. So Gavin, your run should have
> stayed around the starting position. Make the histogram directly and
> you should get a better idea.
> Chris.
> -- original message --
> To clarify, the tutorial sets "pull_init1 = 0" because it is used in
> conjunction
> with "pull_start = yes," in order to take the starting COM distance as
> the
> reference.  Check the grompp output to verify that you're getting what
> you think
> you should be.  Otherwise, you'd have to set "pull_start = no" and
> modify your
> .mdp file to reflect the proper value of pull_init1 for every window.
> -Justin

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