[gmx-users] How good to use triclinic box for gormacs simulations?

[João Henriques]

Hi,

How does the link to "editconf" help in answering the original question?

Anyway, no, there is no specific recipe to select a box type. You generally
have to make an educated guess by using your scientific intuition and
knowledge about the shape (and conformational plasticity) of your system.
Then as the simulation runs, you keep checking the system's integrity to
see if it holds (is it interacting with its image?, etc). No box is
inherently inferior to another, it all depends on your system and how much
computational effort a particular box shape will save you (without
compromising the simulation).

Cheers,
J

On Tue, Oct 31, 2017 at 7:39 AM, Kunal Dutta <
kunal_lifesc at mail.vidyasagar.ac.in> wrote:

> Hi,
> Please check the link.
> http://manual.gromacs.org/programs/gmx-editconf.html
> Best, Kunal
>
>
> On Tue, Oct 31, 2017 at 3:22 AM, vijayakumar gosu <
> vijayakumargosu at gmail.com
> > wrote:
>
> > Hello all,
> >
> >
> > I have performed simulations for Protein RNA complex around 1500
> residues.
> > I have used triclinic box with 1.4 nm distance from the edge of the box
> to
> > protein as triclinic box takes less number of water molecules (~100000)
> > compared to other boxes . The simulation results looks fine and i am able
> > to answer the biological question. however i have not seen many
> > publications using triclinic box. Hence i am bit skeptical and like to
> > know  there is any criteria to choose the simulation box.
> >
> >
> > Thanks
> > --
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>
> --
> ---------------------------------------------------------
> Regards.
> Kunal Dutta
> Senior Research Scholar
> Microbiology and Immunology Laboratory
> Department of Human Physiology with Community Health
> Vidyasagar University, Medinipur-721102
> West Bengal, India.
> Cell: 9126181933
> --------------------------------------------
> ORCID ID: 0000-0002-0818-8787
> RG: https://www.researchgate.net/profile/Kunal_Dutta2
> GS: https://scholar.google.co.in/citations?user=ULby284AAAAJ&hl=en
>
> --
>
>
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