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

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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