VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 01 2012 - 17:04:37 CDT

• Next message: Heather Mayes: "Re: Make "Load all at once" the default? Adding representations?"
• 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"
• Next in thread: Jeffrey Potoff: "Re: Problem with moving protein for all frames"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Tue, May 1, 2012 at 5:14 PM, gökçe ayşe güven <gguvenster_at_gmail.com> 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?

"didn't work" is not a very useful statement.

the pbctools plugin *should* work (if you use it
correctly), and is the recommended option.

to get help, you have to provide more details
about what exactly you did, what the result
was and then people can give more specific
instructions.

also, this is a rather frequently occurring
problem. i would recommend to search
through the mailing list archives for older
messages on the subject.

cheers,
    axel.

> --
> Gökçe Ayşe Güven

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.

• Next message: Heather Mayes: "Re: Make "Load all at once" the default? Adding representations?"
• 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"
• Next in thread: Jeffrey Potoff: "Re: Problem with moving protein for all frames"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]