[gmx-users] combine two gro into one

Sikandar Mashayak symashayak at gmail.com
Fri May 14 05:19:56 CEST 2010

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....


On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul <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
> 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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