[gmx-users] combine two gro into one

Justin A. Lemkul jalemkul at vt.edu
Fri May 14 05:02:59 CEST 2010

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 :)


> 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


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