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