From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Fri Nov 04 2005 - 14:59:17 CST
As explained in the NAMD tutorial, "one should work with a box which
is large enough that the protein does not interact with its image in the
next cell if periodic boundary conditions are used" (if you are not using
periodic boundary conditions, you should be careful with boundary effects
When full electrostatic is not being used, a good criteria is the
cutoff used for non-bonded interactions (usually ~ 12-13 AA as recommended
by developers of parameters). If you have a water box 15 AA larger in each
side of the protein, then the distance between periodic images of the
protein would be about 30 AA, which should be OK. Note that this distance
may change if you use constant pressure, specially at the beginning of
simulations when the box will shrink to get an appropriate
pressure/volume. When using full electrostatic, you should be more
careful, specially if your protein is highly charged and/or if your water
box does not have any ions to screen electrostatic interactions.
Furthermore, and as also pointed out in the tutorial, "if the protein is
being pulled, the box should be large enough that the water will still
significantly immerse the protein when it is fully extended"
Last, but not least, it would be good to remind all the first warning of
the tutorial: "The goal of this tutorial is to introduce NAMD by
performing some short molecular dynamics simulations. Therefore, the
examples provided are optimized so simulations can be done in a reasonable
period of time on a common computing facility. This means that some
parameters and conditions under which simulations are done in this
tutorial are not suitable for scientific studies. Whenever this happens it
will be pointed out and alternatives or more appropriate
parameters/conditions will be provided in case you want to improve the
simulations and/or you have more computer power available"
Let us now if you have more questions, or if alternative
parameters/conditions are not provided in the tutorial.
On Fri, 4 Nov 2005, santanu chatterjee wrote:
> is there any way of deciding what size of water box
> (i.e., how many water molecules) should be used to
> solvate any protein? In NAMD tutorial, Ubiquitin is
> solvated using 5 AA water box in each side of the
> molecule. Ubiquitin is of size nearly 600 atoms. Is
> that sufficient for any molecule of similar size?
> Thanks in advance,
> Enjoy this Diwali with Y! India Click here http://in.promos.yahoo.com/fabmall/index.html
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