[gmx-users] Box Size in MD

Lara Bunte lara.bunte at yahoo.de
Fri Apr 13 12:12:42 CEST 2012

Hi Justin

What is a box vector? I read that the CHARMM force field that I am using has a cut-off of 1 (is this Angstrom or nano-meters?). So should I use a box size of 3 nano-meters? 


 Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 17:28 Donnerstag, 22.März 2012
Betreff: Re: [gmx-users] Box Size in MD

Lara Bunte wrote:
> Hello
> What size should a box have in that you do your MD? I always read that for
> short Lennard Jones interactions one should do a cut off with the half of the
> box size but what how to know a good box size?

This is not correct.  The cutoffs are dictated by the force field you've chosen to use.  There are predefined values that should (for the most part) be adhered to.  What you need to make sure of when setting up the box is that the longest cutoff cannot exceed half the shortest box vector.  If it does, you get duplicate force evaluations from a violation of the minimum image convention. Use of an NPT ensemble will cause the box dimensions to fluctuate (due to pressure) and thus it is unwise in such cases to ever have a box that is only twice the size of the longest cutoff, as violations are almost certain to occur.


-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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