[gmx-users] fix simulation box corners NVE

[Mark Abraham]

Hi,

And if you care, the solution is to post-process with trjconv, e.g.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
mdrun does whatever is computationally convenient, rather than speculating
which representation people would like.

Mark

On Tue, Jan 5, 2016 at 6:33 AM Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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