[gmx-users] Volume and boundary Questions

[Tsjerk Wassenaar]

Hey :)

You can define any box 'shape', expressed in terms of the corresponding
lattice vectors, compliant with the rules stated in chapter 3 of the
manual. You can set a hexagonal prism cell using editconf, using the -box
and -angles options. In your case, the long edge should be along x, and has
90 degree angles with the other two vectors. It will end up something like
(fill in your own lengths)

gmx editconf -box 25 5 5 -angles 90 90 60

Hope it helps,

Tsjerk

On Fri, Mar 18, 2016 at 12:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/17/16 3:01 PM, ANAND AMITKUMAR DHARIA wrote:
>
>> Hello,
>>
>> I have two questions about setting up my box for simulation. Thank you for
>> any and all input in advance.
>>
>> 1. Is the simulation box dimensions and volume fixed throughout the
>> simulation (or are they allowed to fluctuate around the set dimensions)?
>>
>>
> That depends on the ensemble you choose for the simulation.  NVT = fixed
> box size.  NPT = the box size varies in response to pressure.
>
> 2. Is it possible to make custom box shapes (hexagonal) for a simulation
>> run instead of using the gromacs supported box types?
>>
>>
> If it's not supported, it's not supported.
>
> -Justin
>
> Context on my questions is that I would like to simulate proteins in
>> restrained nanotubes, where the tubes are the dimensions of the simulation
>> box (this way the entire system will look continuous with no space, when
>> periodic boundaries are applied).
>>
>> Please let me know if I need to clarify further.
>>
>> Thanks,
>> AD
>>
>>
> --
> ==================================================
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.