[gmx-users] combine two gro into one

[Justin A. Lemkul]

Sikandar Mashayak wrote:
> yeah I know its simple, but only concern I have is that, the index of 
> atom/residue in two files may not be in agreement, so I have to 
> change/shift index of atoms in one of the file.
> 
> but anyway I guess I will have to do it manually....
> 

That part can be done with genconf -renumber.

-Justin

> thanks
> sikandar
> 
> On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Sikandar Mashayak wrote:
> 
>         I need to do water channel simulations... I have two gro files
>         with me...one for wall atoms and one for water atoms...assuming
>         the co-ordinates of atoms are appropriate, I just need to rename
>         the indices of each atom appropriately and append one file to
>         another....I plan to do it by hand...but it will be great if
>         there is an automatic way of doing it in gromacs?
> 
> 
>     This is a simple task that can be done with the Unix 'cat' command.
>      Thus there is no Gromacs tool that reproduces this function.  A few
>     seconds with a text editor after concatenation to remove unnecessary
>     title lines and box vectors and you're done, assuming (as you've
>     said) that all the coordinates are appropriately defined.  The whole
>     process probably takes less typing than sending this email :)
> 
>     -Justin
> 
>         thanks
>         sikandar
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

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

========================================