[gmx-users] Uniform Distribution of drug molecules inside water spc216

Justin A. Lemkul jalemkul at vt.edu
Wed Oct 12 17:57:47 CEST 2011

meisam valizadeh kiamahalleh wrote:
> Dear GMX users
> Good day to you
> I have some drug molecules (cisplatin) added manually and 
> randomly inside a system which is going to be solvated in spc216 water. 
>  I used genbox command to add the correct number of water molecules 
> needed to solvate the box. The drug molecules are located very closed to 
> each other. Kindly, would you please let me know how I can distribute 
> drug molecules uniformly among the water molecoules to obtain a 
> certain concentration of the drug? May I know if there is any specific 
> tool or script which can help me to do it?

I don't know how you did the initial insertion, but genbox -ci -nmol will add 
molecules randomly, after which you can solvate with water.  Don't combine these 
steps.  Do the insertion, then add the water.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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