[gmx-users] Volume and boundary Questions
jalemkul at vt.edu
Fri Mar 18 12:58:31 CET 2016
On 3/17/16 3:01 PM, ANAND AMITKUMAR DHARIA wrote:
> 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.
> 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.
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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