[gmx-users] Boundary

[Justin A. Lemkul]

On 7/6/12 3:06 PM, dariush wrote:
> Hi all,
>
> Why does GROMACS just provide PBC for boundary condition?
> However, LAMPPS as an example provides four kind of boundary:
> periodic, non-periodic and fixed, non-periodic and shrink-wrapped and
> non-periodic and shrink-wrapped with a minimum value.
>

Gromacs can also do non-periodic systems by setting "pbc = no" in the .mdp file. 
  A variety of options exist for walls, as well.

If there are particular features that users want, they are welcome to implement 
them and submit them for review in the development code.  Otherwise, if no one 
files a feature request on redmine, the developers aren't going to invest time 
in the feature unless they need it themselves.  I would hazard a guess that 3-D 
periodic boundary conditions are the most commonly used in simulations of 
biomolecules.

> PBC makes problem when you want to make movie in VMD, even you add some
> mirror-wise molecule in each direction.
>
> Is there anyway to figure out this problem?
>

Any trajectory can be "fixed" for visualization purposes with trjconv.  You may 
need several iterations to achieve the desired effect.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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