[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?
a.nash at ucl.ac.uk
Mon Mar 14 23:31:57 CET 2016
Is there a way of keeping the x, y box dimensions fixed during an NPT
simulation, with changes to volume only changing in the Z dimension?
Semiisotropic is not quite working out, see below.
Context: I want a coiled-coil dimer aligned in the Z direction. Each
coiled-coil will see it¹s explicit neighbour, plus all period images. This
will give an impression of a collagen fibrillar environment. Each protein
should not be be able to tilt off the z-axis, due to the packed nature.
Either end of the two coiled coils will be Œbulk¹ water which can expand
and contract from changes in volume. If the x or y dimension changes there
is a risk to water forming a layer between an explicit coiled-coil and one
of its period images, thus losing the fibrillar environment effect.
Dr Anthony Nash
Department of Chemistry
University College London
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