[gmx-users] Re: Removal of pbc for analysis

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 17 12:33:32 CEST 2008

alkasrivastava at iitb.ac.in wrote:
> Hi All,
> I am doing a 5 peptide simulation, and i want to analyze some of the basic
> properties like radius of gyration, distance between peptides etc. but i
> wanted to do it in a situation when all my peptides are inside the box.
> Due to pbc i am getting artifacts. i tried all the -pbc option (inbox,
> whole, nojump, etc) as well as all the -center option and a combination of
> both for converting trajectory by trjconv  but i am not getting what i
> want. I want all of my peptides to be present in the box and that to in
> whole form not broken so that my analysis give me a true reflection of
> what is happening. If anyone can help me.

Well, you're not mentioning how you're doing it (commands!), so otherwise we'd 
just shrug our shoulders and say, "you've tried everything, so I guess nothing 
works!"  Sorry to say that trjconv is one of the most difficult tools to provide 
help with, so without actually seeing the results of what you're doing, the best 
advice is to just keep playing with it.  Sometimes my fitting procedures have 
taken four or five iterations of different options!

I have done some simulations of multiple peptides/proteins and the like, and a 
simple -pbc nojump has always worked just fine.  Otherwise, try -pbc mol/res 
under GMX 3.3.3.  Centering probably won't work very well, since there are 
multiple peptides.


> Thanks
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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