[gmx-users] genbox with mixture solvent

YQ Liu yqliu at sunm.shcnc.ac.cn
Thu Sep 19 09:16:17 CEST 2002

>> 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.

Thanks very much for your help!  However,still I wonder how to setup such a mixture system.
genbox -cp protein.gro -cs -ci small_mol.gro -nmol N -p protein.top -o out.gro
genbox -cp protein.gro -cs ???.gro  -p protein.top -o out.gro
how to generate ???.gro present as solution?
Thanks again!
        YQ Liu
        yqliu at sunm.shcnc.ac.cn

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