[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?

Justin Lemkul jalemkul at vt.edu
Mon Mar 14 23:34:28 CET 2016

On 3/14/16 6:31 PM, Nash, Anthony wrote:
> Hi all,
> 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.

Set compressibility = 0 for x-y.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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