[gmx-users] option -pbc in trjconv

[Mark Abraham]

On 3/06/2011 6:48 PM, Kavyashree M wrote:
> Dear Sir,
>
>   I used dodecahedron for the simulation. My specific doubt was whether
> do we need to modify the .xtc file using some options of -pbc like 
> nojump,
> mol, before going for analysis or we can directly go for analysis 
> using the
> raw .xtc file.

Maybe. Only a general answer can be given to a general question.

Mark

> Thanking you
> With regards
> M. Kavyashree
>
>
>
>     ---------- Forwarded message ----------
>     From: *Mark Abraham* <Mark.Abraham at anu.edu.au
>     <mailto:Mark.Abraham at anu.edu.au>>
>     Date: Fri, Jun 3, 2011 at 12:58 PM
>     Subject: Re: [gmx-users] option -pbc in trjconv
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>
>
>
>     On 3/06/2011 3:42 PM, Kavyashree M wrote:
>
>         Dear users,
>
>             I wanted to ensure that the option of -pbc in trjconv is
>         only for visualization,
>         and if I do all possible calculations with the original .xtc
>         file there wont be any
>         problem.
>
>
>     -pbc is for any purpose you can think of. Some analyses of
>     periodic simulations only make sense for some representations of
>     the unit cell. Some don't. Read about the tool, think carefully,
>     then act :-)
>
>     Mark
>     -- 
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>
>     -- 
>     Yours Sincerely,
>     Dr. Shankar Prasad Kanaujia
>     Research Associate
>     C/O - Professor K. Sekar
>     Bioinformatics Centre
>     Indian Institute of Science, Bangalore-12
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>

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