[gmx-users] water/cosolvent

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 23 10:59:27 CET 2002

On Wed, 23 Jan 2002, Marc Lensink wrote:

>Hi all,
>does anybody happen to have an equilibrated box of water with a
>medium-sized hydrophobic cosolvent lying around?
>I would be looking for water with 5 to 10 mol% of t-butanol or
>1-butanol or so.
I don't ave any lying around anymore, but it is really easy to make...
Take the decane+water system (topology and coordinate in share/top)
Modify the topology to change C5 into OA, and C6 into HO, take out the 
extra dihedrals, angles and bonds.
Use grep -v C7 dec.gro | grep -v C8 | grep -v C9 | grep -v C10 > new.gro

minimize, done. 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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