[gmx-users] option -pbc in trjconv

[Kavyashree M]

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.

Thanking you
With regards
M. Kavyashree


>
> ---------- Forwarded message ----------
> From: Mark Abraham <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>
>
>
>
> 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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