[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?
a.nash at ucl.ac.uk
Mon Mar 14 23:37:20 CET 2016
Justin, that’s awesome. Thanks
On 14/03/2016 22:34, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Justin Lemkul"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
jalemkul at vt.edu> wrote:
>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.
>> will give an impression of a collagen fibrillar environment. Each
>> 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
>> is a risk to water forming a layer between an explicit coiled-coil and
>> 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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