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On 6/02/2012 11:09 PM, Anushree Tripathi wrote:
<blockquote
cite="mid:CAAx43BzE=yB3FK=2LcKTmUL9+tmpJ_hb6WqrX6iBmd60p8qqBQ@mail.gmail.com"
type="cite">Will you please send me the basic tutorial in which I
can find how to use -n option in " grompp -f nvt.mdp -c em.gro -p
topol.top -o nvt.tpr" command.<br>
</blockquote>
<br>
All the tutorials provide examples of using the general syntax<br>
<br>
command -x value -y file.ext<br>
<br>
for various values of command, x, value, y and file.ext. These allow
you to provide the command with the input to work on and the
instructions for how to act. The option (x and y) provides a label
for the values, so that you and the command both know what is input,
or output, etc. command -h provides a list of all the options, and
indicates the kind of data they might wish to have supplied with
them.<br>
<br>
You seem to be trying to do a membrane simulation. Likely any
membrane simulation will have to deal with the issue of temperature
coupling and the lipid group. You should complete any such tutorials
you can find and understand them fully.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAAx43BzE=yB3FK=2LcKTmUL9+tmpJ_hb6WqrX6iBmd60p8qqBQ@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Mon, Feb 6, 2012 at 5:17 PM, Justin A.
Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
Anushree Tripathi wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
where should I use -n option in the command (i.e., grompp
-f nvt.mdp -c em.gro -p topol.top -o nvt.tpr).Please tell
me.<br>
<br>
</blockquote>
<br>
</div>
I would suggest you refer to grompp -h and/or go through some
basic tutorial material so that you can get a feel for command
line options and how to apply them.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">
On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham <<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>
<mailto:<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>
wrote:<br>
<br>
On 6/02/2012 8:28 PM, Anushree Tripathi wrote:<br>
<br>
Inspite of having DPPC in index file,when I run the
command (<br>
i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o
nvt.tpr ),I am<br>
getting the error:<br>
<br>
Group DPPC not found in indexfile.<br>
Maybe you have non-default goups in your .mdp file,
while not<br>
using the '-n' option of grompp.<br>
In that case use the '-n' option.<br>
<br>
Now, what to do? Please guide me.<br>
<br>
<br>
You seem not to have used the -n option. You could try
using it. :)<br>
<br>
Mark<br>
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<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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