[gmx-users] genbox with mixture solvent

David spoel at xray.bmc.uu.se
Thu Sep 19 08:23:24 CEST 2002

On Thu, 2002-09-19 at 07:44, YQ Liu wrote:
> Dear All:
>      I have faced a problem in setuping a simulation system with genbox program.
>      My simulation system consists a protein  bathed in a mixture solvent which includes water and a kind of small molecule. My problem is that when I use genbox program following:
> genbox -cp protein.gro -cs -ci small_mol.gro -nmol 500 -p protein.top -o out.gro
> It seems that genbox do not check the VDW contact conflictions between protein molecule and my inserted small molecules. The genbox only check and remove VDW contact conflictions between protein and solvent or between solvent and solvent. Is my procedure right? Or try some other program? How can I setup such a mixture solvent system with protein bathed in?
>      Thanks for any possible suggestion.
it sounds not correct as you say it. What you can do anyway is make a
solution of your small molecule (i.e. small mol + water) and solvate the
protein in that.
>         YQ Liu
>         yqliu at sunm.shcnc.ac.cn
>           2002-09-19
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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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