[gmx-users] Umbrella sampling ignore hydrogen command -ignh

Chris Papamitrou cpapamit at aggies.ncat.edu
Thu Nov 6 22:53:49 CET 2014

I am trying to perform a simulation regarding the effect that hydration has
on tensile response for my system.  When i looked into the umbrella
sampling tutorial it said to create a start file using the

pdb2gmx -f input.pdb -ignh -ter -o complex.gro

command and was wondering what effect that the -ignh option had on my
simulated results?  do the hydrogens
not get accounted for in this simulation, and if so, how are the
atomic bonds in which the hydrogens are
supposed to be located treated in terms of replacing those hydrogens?
does this mean i am doing a
united atom model ?

*"The simplicity of nature is not to be measured by that of our
conceptions.  Infinitely varied in its effects, nature is simple only in
its causes, and its economy consists in producing a great number of
phenomena, often very complicated, by means of a small number of general

*--Pierre Simon de Laplace*

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