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

[Nash, Anthony]

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.
>>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
>
>-- 
>==================================================
>
>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
>http://mackerell.umaryland.edu/~jalemkul
>
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