Sure!<br>My code is <br><br>#!/bin/bash<br>for ((i=1; i<=357; i=$i+3))<br>do<br>trjconv -f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o ../cg_gro/300-${i}.gro -pbc whole<br>done<br><br>very stupidly I just need to type 0 all the time in the interactive window that trjconv opens.<br>
Any help?<br>Thanks<br><br><div class="gmail_quote">2012/2/3 lina <span dir="ltr"><<a href="mailto:lina.lastname@gmail.com">lina.lastname@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Yes but those tips are not for bash scripts... :(<br>
</blockquote>
<br></div>
You'd better post what you have done so far about this script,<br>
<br>
probably someone can help you improve or refine it.<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<br>
2012/2/3 Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>><div class="im"><br>
<br>
On 4/02/2012 12:21 AM, francesca vitalini wrote:<br>
<br>
Hi!<br>
I have to use the gromacs command trjconv to obtain a .gro file<br>
from a .xtc and a .pdb file. I have to do it for several files<br>
in a bash for loop so I'd rather prefer to find a way to make my<br>
script type in the trjconv interactive terminal always the same<br>
number for the system. Any tips?<br>
<br>
<br>
Check out<br></div>
<a href="http://www.gromacs.org/__Documentation/How-tos/Using___Commands_in_Scripts" target="_blank">http://www.gromacs.org/__<u></u>Documentation/How-tos/Using___<u></u>Commands_in_Scripts</a><div class="im"><br>
<<a href="http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts" target="_blank">http://www.gromacs.org/<u></u>Documentation/How-tos/Using_<u></u>Commands_in_Scripts</a>><br>
<br>
Mark<br>
<br>
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