[gmx-users] fix simulation box corners NVE

[Sereda, Yuriy Vladimirovich]

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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