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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 13 00:24:08 CEST 2011

On 13/10/2011 2:13 AM, 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?

Decide how many drug molecules you want in a box of a given size, and 
place one in a much smaller box. Then use genconf to replicate that 
small box up to the proper size. Use the genconf option to randomize the 
orientation, solvate with genbox, then equilibrate for a long time.


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