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

    ========================================


--
========================================

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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