VMD-L Mailing List
From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Tue May 01 2012 - 19:53:12 CDT
- Next message: meisam valizadeh kiamahalleh: "Free software for building peptide"
- Previous message: Axel Kohlmeyer: "Re: Make "Load all at once" the default? Adding representations?"
- In reply to: gökçe ayþe güven: "Problem with moving protein for all frames"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
On 5/1/2012 5:14 PM, gökçe ayşe güven wrote:
> Hi all,
>
> I have 400ns simulation for 1mrp protein system and after 140ns half
> of my protein system moves out of the PBC cell, for that reason, -for
> specific frames- distance between 2 selected atoms (Fe iron and Glu
> residue CA atom) jumps 60 angstrom in 2ps which is impossible. In
> short, I want to keep my protein at the center of my PBC cell for all
> frames. I tried moveby, pbctools, etc. but they didn't work. Could
> anybody help me please?
> --
> Gökçe Ayşe Güven
It is (also) relatively easy to solve this problem using the GROMACS
trajectory manipulation tool trjconv
http://manual.gromacs.org/current/online/trjconv.html
http://www.chem.purdue.edu/slipchenko/courses/chem579/files/lab4/vmd-exercises.pdf
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu ======================================================================
- Next message: meisam valizadeh kiamahalleh: "Free software for building peptide"
- Previous message: Axel Kohlmeyer: "Re: Make "Load all at once" the default? Adding representations?"
- In reply to: gökçe ayþe güven: "Problem with moving protein for all frames"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
