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.
Mark
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
