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.
Mark
Greetings
Lara
------------------------------------------------------------------------
*Von:* Justin A. Lemkul <[email protected]>
*An:* Lara Bunte <[email protected]>; Discussion list for GROMACS
users <[email protected]>
*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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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