[gmx-users] generate solvents

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 26 12:32:30 CET 2005

Rongliang Wu wrote:

>Hello gmx-users,
>	since i can generate a pure solvent of water easily with "genbox -cs spc216.gro -box i j k", how can i generate a solvent or mixed solvent of anthing else? i wonder how i can gennerate a box of solvents like spc216.gro, which can be used for generating solvents with genbox, from a single molecule? are there any strict constraints if i use -ci and -nmol, for the system i used to generate with -ci and -nmol does not work normally.  
I f you want mixed solvents then make a small box first, equilibrate 
that and then hand that to genbox instead of spc216. Note that solvent 
molecules in genbox have to consist of a single "residue".

>Rongliang Wu
>State Key Laboratory
>of Polymer Physics and Chemistry
>Center of Molecular Science
>Institute of Chemistry
>Chinese Academy of Sciences
>          wurl04 at iccas.ac.cn
>          2005-11-26
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list