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 <jalem...@vt.edu
<mailto:jalem...@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
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