[gmx-users] fix simulation box corners NVE

[Tsjerk Wassenaar]

Hi Yuri,

Sure. Which positions are used during the run and written out depends on
the box and whether you use domain decomposition or not.

Cheers,

Tsjerk
On Jan 4, 2016 11:15 PM, "Sereda, Yuriy Vladimirovich" <ysereda at indiana.edu>
wrote:

> Thanks, this helps a bit, now I can be more specific:
> does particle ever cross the boundary of the box as given by the lattice
> vectors (last row in *.gro frames ?) 0..Lx, 0..Ly, 0..Lz during NVT or NVE?
> E.g., can x, y, or z become <0 ?
> Yuri
> ________________________________________
> От: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> от имени Tsjerk
> Wassenaar <tsjerkw at gmail.com>
> Отправлено: 4 января 2016 г. 16:58
> Кому: Discussion list for GROMACS users
> Тема: Re: [gmx-users] fix simulation box corners NVE
>
> Hi Yuri,
>
> You have to distinguish between the systems lattice vectors and the
> positions of particles. The lattice remains fixed in NVE and NVT, but the
> particles are at many positions at the same time, and any position is good
> enough for putting in the XTC/TRR/GRO/PDB file.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Mon, Jan 4, 2016 at 10:42 PM, Sereda, Yuriy Vladimirovich <
> ysereda at indiana.edu> wrote:
>
> > How to fix corners of the NVE or NVT Gromacs simulation box?
> >
> > How to transform existing trajectory to comply with this?
> >
> > How to set parameters of a new Gromacs simulation to make sure simulation
> > box corners stay at fixed positions?
> >
> > Thanks,
> >
> > Yuri
> >
> > IU Bloomington Chemistry
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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