[gmx-users] Umbrella sampling question
gmxquestions at gmail.com
Tue Nov 13 18:54:58 CET 2012
I'm a new poster on the maillist, and new to umbrella sampling but not to
MD in general.
I have recently done some pulling simulation with Gromacs, but have a few
questions about the outcome, and in particular the distances that are
calculated for the different windows. I realize this is a question that has
come up before, and there are some useful posts in the archives, but
nothing that exactly answers my questions.
To begin, I ran a pulling-simulation pulling a molecule starting in the
middle of a membrane (and inside a protein transport channel) straight up
in z. To that end, I used the following mdp-settings:
pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_ngroups = 1
pull_start = yes
pull_group0 = Protein
pull_group1 = pg1
pull_rate1 = 0.001
pull_k1 = 500
So my pull groups are the COM of the protein, and one atom named pg1 on the
To my understanding, this should pull the pg1-molecule straight up in z,
and that is indeed also what is happening in the simulation.
I ran this simulation for 6 ns, and it resulted in about 40 separate
conformations to use for umbrella sampling. All of those simulations also
seem to work, I can use the resulting pullf,xvg-files as input to g_wham,
and get a histogram-plot with reasonable overlaps.
However, I'm trying to understand how the various distances relate to each
other. For example, in the profile.xvg-file I get a z-distance for the
first frame as 1.761971 nm, while checking with g_dist gives me 1.80833
(for z). Continuing a few frames further, there are still differences, and
they appear to be random.
How are the distances in the profile.xvg-file computed? The average of the
dZ column of the pullx-file for the first frame is 1.75787, which is sort
of close to 1.761971, but not quite (and also for the next frames there is
Sorry if this became a long mail, but I need to understand this in order to
be able to progress with my research.
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