[gmx-users] On using CO2 as solvent

Justin Lemkul jalemkul at vt.edu
Fri May 24 00:28:09 CEST 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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