[gmx-users] combine two gro into one
Justin A. Lemkul
jalemkul at vt.edu
Fri May 14 05:20:31 CEST 2010
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.
> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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