[gmx-users] trjconv select group

[lina]

On Friday 03,February,2012 10:02 PM, francesca vitalini wrote:
> Sure!
> My code is
>
> #!/bin/bash
> for ((i=1; i<=357; i=$i+3))
> do
> trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o
> ../cg_gro/300-${i}.gro -pbc whole


try touch a file as index.txt and put 0 in the index.txt

trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o 
../cg_gro/300-${i}.gro -pbc < index.txt

> done
>
> very stupidly I just need to type 0 all the time in the interactive
> window that trjconv opens.
> Any help?





> Thanks
>
> 2012/2/3 lina <lina.lastname at gmail.com <mailto:lina.lastname at gmail.com>>
>
>     On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:
>
>         Yes but those tips are not for bash scripts... :(
>
>
>     You'd better post what you have done so far about this script,
>
>     probably someone can help you improve or refine it.
>
>
>
>
>
>         2012/2/3 Mark Abraham <Mark.Abraham at anu.edu.au
>         <mailto:Mark.Abraham at anu.edu.au>
>         <mailto:Mark.Abraham at anu.edu.__au <mailto:Mark.Abraham at anu.edu.au>>>
>
>
>             On 4/02/2012 12:21 AM, francesca vitalini wrote:
>
>                 Hi!
>                 I have to use the gromacs command trjconv to obtain a
>         .gro file
>                 from a .xtc and a .pdb file. I have to do it for several
>         files
>                 in a bash for loop so I'd rather prefer to find a way to
>         make my
>                 script type in the trjconv interactive terminal always
>         the same
>                 number for the system. Any tips?
>
>
>             Check out
>         http://www.gromacs.org/____Documentation/How-tos/Using_____Commands_in_Scripts
>         <http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts>
>
>         <http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts
>         <http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts>>
>
>             Mark
>
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