[gmx-users] minimum periodic distance

Daniela S. Mueller d.s.mueller at rug.nl
Mon Feb 13 01:03:45 CET 2006


if the distance between periodic images is less than your interaction 
range, the molecule is going to interact with itself across the boundary 
- which you want to avoid.

you can measure the minimum periodic distance for a structure or 
trajectory, but you can't 'set' it. make sure that your box is large 


Wang Zhun wrote:
> Hi, all,
> In a previous post
> http://www.gromacs.org/pipermail/gmx-users/2004-January/008561.html
> "use g_mindist -pi to chech the 'minimum periodic distance'  to its periodic images during the simulation. That should be at least 1 nm, but for PME maybe one would want that larger."
> I wonder how 1nm is set. Is this value based on rvdw, rlist, etc? If  the minimum periodic distance is far less than 1nm, what does it imply? Is a  larger box needed to start MD?
> Thanks.
> BTW, in my former post there is a typo: editconf command should generate a "tric" box, not a "cubic" one, if box type is not set.


Daniela S. Mueller

Diplom biologist

-Molecular Dynamics Group, UQ -

School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane

Phone: +61-7-33653732
Email: d.s.mueller at uq.edu.au

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm


- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md

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