[gmx-users] Box Size in MD

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 13 12:30:01 CEST 2012

On 13/04/2012 8:12 PM, Lara Bunte wrote:
> Hi Justin
> What is a box vector?

See manual 3.2. See tutorial material for different ways of making boxes.

> I read that the CHARMM force field that I am using has a cut-off of 1 
> (is this Angstrom or nano-meters?).

That's a totally separate concept, but can contribute to the box size 
decision. Probably that source meant 1nm, since a cutoff that is shorter 
than a C-C bond would be pretty useless as a model. Never just take a 
number out of context or without dimensions, or you'll curse yourself later.

> So should I use a box size of 3 nano-meters?

We can't tell on the information you've given - and you should decide 
for yourself after familiarizing yourself with GROMACS workflows and 
thinking about what you need for your simulation, and comparing your 
proposed setup with what others have done in published work.


> Greetings
> Lara
> ------------------------------------------------------------------------
> *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
> -- ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120413/af3c23a3/attachment.html>

More information about the gromacs.org_gmx-users mailing list