[gmx-users] fix simulation box corners NVE

[Erik Marklund]

The system is still periodic, so particles can indeed cross the boundaries. This is a good thing in the majority of cases, because the alternative, where particles are trapped, gives rise to really severe boundary effects.

Kind regards,
Erik

> On 4 Jan 2016, at 22:15, 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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> 
> 
> 
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> Tsjerk A. Wassenaar, Ph.D.
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