VMD-L Mailing List
From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Thu May 15 2008 - 15:23:51 CDT
- Next message: Khaled Barakat: "How to calculate the volume of a molecule using vmd?"
- Previous message: Yinglong Miao: "Truncated Octahedron for VMD and NAMD simulation"
- In reply to: Yinglong Miao: "Truncated Octahedron for VMD and NAMD simulation"
- Next in thread: Vlad Cojocaru: "Re: Re: namd-l: Truncated Octahedron for VMD and NAMD simulation"
- Reply: Vlad Cojocaru: "Re: Re: namd-l: Truncated Octahedron for VMD and NAMD simulation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
1) Check out the Gromacs manual for how to specify the vectors of the
unit cell for the truncated oct.
2) Make an estimate on how big the length of an edge of the oct. would
be, enter the values of the cell vectors in an Namd configuration file
and let your system equilibrate with NPT for a 1-2ns. Specify
"wrapnearest on" and, in the end, you will get truncated oct. shaped sytem.
I hope this helps,
George
-- ________________________________________________________________________ George Madalin Giambasu PhD Student University of Minnesota Phone : (612) 625-6317 Department of Chemistry Fax : (612) 626-7541 207 Pleasant St. SE e-mail: Minneapolis, MN USA 55455-0431 GeorgeMGiambasu_at_umn.edu York Research Group giambasu_at_gmail.com http://theory.chem.umn.edu/ ________________________________________________________________________
- Next message: Khaled Barakat: "How to calculate the volume of a molecule using vmd?"
- Previous message: Yinglong Miao: "Truncated Octahedron for VMD and NAMD simulation"
- In reply to: Yinglong Miao: "Truncated Octahedron for VMD and NAMD simulation"
- Next in thread: Vlad Cojocaru: "Re: Re: namd-l: Truncated Octahedron for VMD and NAMD simulation"
- Reply: Vlad Cojocaru: "Re: Re: namd-l: Truncated Octahedron for VMD and NAMD simulation"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]