[gmx-users] inquiring for solving trjconv problems

[Justin Lemkul]

On 1/21/13 11:00 AM, Mehdi Bagherpour wrote:
> hello justin
>
> I used *make_ndx -f md.tpr:
>
>    0 System              : 35194 atoms
>    1 DNA                 :  1012 atoms
>    2 MG                  :     4 atoms
>    3 CL                  :    29 atoms
>    4 K                   :    51 atoms
>    5 Water               : 34098 atoms
>    6 SOL                 : 34098 atoms
>    7 non-Water           :  1096 atoms
>    8 Other               :     4 atoms
>    9 MG                  :     4 atoms
>   10 CL                  :    29 atoms
>   11 K                   :    51 atoms
>   12 Ion                 :    80 atoms
>   13 MG                  :     4 atoms
>   14 CL                  :    29 atoms
>   15 K                   :    51 atoms
>   16 Water_and_ions      : 34178 atoms
>
>   nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
>   'a': atom        &   'del' nr         'splitres' nr   'l': list residues
>   't': atom type   |   'keep' nr        'splitat' nr    'h': help
>   'r': residue         'res' nr         'chain' char
>   "name": group        'case': case sensitive           'q': save and quit
>   'ri': residue index
>
>   > 1
>
> Copied index group 1 'DNA'
>
>   17 DNA                 :  1012 atoms*
>
> then I used from bellow command:
>
> *trjconv -s md.tpr -f md.xtc -n index.ndx -o md_1.xtc -center*
>
> and then:
>
> *trjconv -s md.tpr -f md_1.xtc -n index.ndx -o md.pdb -pbc mol -ur compact*
>
> but problem is not fixed.
>

Because you're not doing anything productive.  You're just copying an existing 
group that has already been demonstrated to be ineffective.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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