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.<br><br>but anyway I guess I will have to do it manually....<br>
<br>thanks<br>sikandar<br><br><div class="gmail_quote">On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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?<br>
<br>
</blockquote>
<br></div>
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 :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
thanks<br>
sikandar<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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