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

[Justin A. Lemkul]

meisam valizadeh kiamahalleh wrote:
> Dear Justin
> Thank you very much for your always prompt reply. Actually, I added many 
> of drug molecules by copying and pasting a single molecule in discovery 
> studio software. I could even move the drug molecules to any desired 
> locations by select and dragging them.  Finally I used the output pdb 
> file from discovery studio as initial structure in Gromacs, but I could 
> not find any option for the molecule uniform distribution.
> 1) May I know if I should use the drug resname or molecule name infront 
> of -nmol?

The -nmol option takes an integer argument.  Please see genbox -h.

> 2) As you mention the method suggested by you would add the drug 
> molecules randomly. then, May I also Know if they can 
> be uniformly distributed in the water after solvation?

You can only build a random configuration with genbox -ci -nmol.  If you want an 
artificially crystalline system, use genconf -nbox to replicate your existing 
drug molecule as many times as you'd like in whatever dimensions you want. 
Either way, you'll have to do sufficient equilibration to get a homogeneous 
system, if it's even possible.  I'd think the latter approach would be worse 
since you're starting from a very highly ordered system.

-Justin

> Thank you very much
> Best regards
> Meisam
>  
> 
>     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
> 
>     --
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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