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

alkasrivastava at iitb.ac.in alkasrivastava at iitb.ac.in
Thu Jul 17 10:55:37 CEST 2008

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.


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