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On 13/04/2012 8:12 PM, Lara Bunte wrote:
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<div>Hi Justin</div>
<div><br>
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<div>What is a box vector?</div>
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<br>
See manual 3.2. See tutorial material for different ways of making
boxes.<br>
<br>
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<div> I read that the CHARMM force field that I am using has a
cut-off of 1 (is this Angstrom or nano-meters?).</div>
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<br>
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.<br>
<br>
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<div> So should I use a box size of 3 nano-meters? <br>
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<br>
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.<br>
<br>
Mark<br>
<br>
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<div>Greetings</div>
<div>Lara</div>
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<hr size="1"> <b><span style="font-weight:bold;">Von:</span></b>
Justin A. Lemkul <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a><br>
<b><span style="font-weight: bold;">An:</span></b> Lara
Bunte <a class="moz-txt-link-rfc2396E" href="mailto:lara.bunte@yahoo.de"><lara.bunte@yahoo.de></a>; Discussion list for
GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Gesendet:</span></b>
17:28 Donnerstag, 22.März 2012<br>
<b><span style="font-weight: bold;">Betreff:</span></b>
Re: [gmx-users] Box Size in MD<br>
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<br>
<br>
<br>
Lara Bunte wrote:<br>
> Hello<br>
> <br>
> What size should a box have in that you do your MD? I
always read that for<br>
> short Lennard Jones interactions one should do a cut
off with the half of the<br>
> box size but what how to know a good box size?<br>
> <br>
<br>
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.<br>
<br>
-Justin<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
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