[gmx-users] Umbrella Sampling - choice of pull-coord?-dim

Lukas Zimmermann luk.zim91 at gmail.com
Sun May 15 00:55:24 CEST 2016

Dear GROMACS users,

I am interested in the role of the mdp parameter pull-coord?-dim when
a particular umbrella window after having generated initial configurations
for, say, the
COM distance between two groups being the reaction coordinate.

I know that these options can be controlled to restrict the actual pulling,
say with geometry distance,  to a subset of the pull vector components, for
instance to enable
aligment of the pull vector with the box dimensions.

However, I do not understand its role when performing umbrella sampling
along the reaction coordinate.
I know that the pull-code then controls the COM distance between the pull
groups with a (usually) harmonic potential, but what effect will
pull-coord?-dim have?

I observe different behavior for my toy system consisting of two methanol
molecules in vacuum.
With all components enables, I need to correct the PMF for entropic
decrease in the PMF,
since the methanol is sampled on a sphere with increasing radius.
If only allowing one component, the PMF will be flat, but different values
for delta G

Also, in the US Tutorial by Justin, the US code uses:

pull_coord1_dim         = N N Y

Is there any particular reason, not to set

pull_coord1_dim         = Y Y Y

here? Would this setting also be justified? Since, as far as I understood
the procedure,  pulling

is just there for generating the initial configurations and US is more or
less independent of this.

Many thanks in advance!


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