On 5/23/13 6:21 PM, Bao Kai wrote:
Hi, all,
Following the tutorial on building biphasic system from Justin, I put the
decane in a box and equilibrated it first. Then I increased the size of
the box.
Then I wanted to put some CO2 molecules to make a biphasic system.
When I used the following command to do that, I can only add 16 co2
molecules, which is really weird.
genbox_d -cp d10_newbox.gro -cs co2.gro -o d10_solv.gro -p d104.top
Resulting image can be found from the following link.
https://www.dropbox.com/s/slvqfrf4gftu9al/CO2_solvent.png
When I used
genbox_d -cp d10_newbox.gro -cs -o d10_solv.gro -p d104.top
More than 4000 water molecules were added.
Could you please tell me what happened here?
The -cs option builds a grid of solvent configurations within the available
volume of the box contained in -cp. Presumably co2.gro either contains only one
molecule in a large box, or it contains molecules that are very far apart. In
contrast, spc216.gro is a typical condensed-phase water configuration with lots
of molecules.
How to use co2 to be the solvent?
The setup depends on exactly what you intend to do. If decane is a liquid, is
CO2? Are you trying to set up a liquid-gas interface? Are you trying to use
CO2 as a liquid (presumably at some very cold temperature)? In any case, you
need to provide whatever you believe to be a reasonable representation of CO2 as
your "solvent" to -cs, or add a predefined number of molecules using -ci -nmol.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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