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On 4/12/2010 6:45 PM, Anirban Ghosh wrote:
<blockquote
cite="mid:AANLkTimkDxgKQgDCp-aeuHH2+xNtD-GDNeKX4ABT0vgL@mail.gmail.com"
type="cite">Thanks a lot for the reply.
<div>But I am getting different results with the two .tpr files
(first and last) using the following commands:</div>
<div><br>
</div>
<div>trjconv -s <b>first.tpr </b>-f test.xtc -o str.gro -dump
10000 -pbc nojump</div>
<div>trjconv -s <b>last.tpr</b> -f test.xtc -o str.gro -dump
10000 -pbc nojump</div>
</blockquote>
<br>
Did you read trjconv -h about -pbc nojump? Notice how when you
didn't give your command lines last time, you didn't get a very
useful answer.<br>
<br>
<blockquote
cite="mid:AANLkTimkDxgKQgDCp-aeuHH2+xNtD-GDNeKX4ABT0vgL@mail.gmail.com"
type="cite">
<div>So which .tpr file should I use?</div>
</blockquote>
<br>
You're trying to measure a membrane thickness. So you want all the
membrane residues in the same box, and don't care about anything
else. There's various ways to use -pbc and -center to achieve this,
depending on what the simulation has done.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTimkDxgKQgDCp-aeuHH2+xNtD-GDNeKX4ABT0vgL@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Anirban</div>
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charset=ISO-8859-1">
<div>
<br>
<div class="gmail_quote">On Sat, Dec 4, 2010 at 12:29 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im">On 4/12/2010 4:33 PM, Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Thanks a lot for the reply.<br>
Actually I am running a protein in lipid bilayer. Now I
want to<br>
calculate the thickness of the bilayer at the end of the
simulation.<br>
So for that I want the last structure (.gro) file. So I
am trying to<br>
dump the last structure using trjconv (with -pbc
option). So to do<br>
this which .tpr file should I supply to trjconv, the
first one or the<br>
last one?<br>
</blockquote>
<br>
</div>
Since you're not using the coordinates in the .tpr file to
extract the last frame and map its coordinates onto the
.tpr's atom names, it can't matter what they are.<br>
<font color="#888888">
<br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Thanks again.<br>
<br>
Anirban<br>
<br>
On 12/4/10, Justin A. Lemkul<<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204,
204); padding-left: 1ex;">
<br>
Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
Thanks a lot Justin for the reply. Yes, I
understand that. But ideally<br>
which structure should be used as the reference,
in a general, the<br>
starting structure or the end structure?<br>
</blockquote>
That's up to you to decide based on what you need to
measure. Do you want<br>
the<br>
RMSD relative to your starting (i.e. crystal/NMR)
structure, or are you<br>
trying<br>
to study how a protein folds, in which case you'd
use the native (end)<br>
state?<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
like when I an using trjconv to dump my last frame
(with "-pbc nojump"),<br>
which .tpr file should I use to get the exact
picture of what has<br>
happened to my protein at the end of the
simulation. Should I use the<br>
first .tpr file or the last .tpr file?<br>
<br>
</blockquote>
I don't understand what you mean. "What has
happened" is an entire<br>
trajectory,<br>
not a snapshot.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt
0pt 0pt 0.8ex; border-left: 1px solid rgb(204,
204, 204); padding-left: 1ex;">
Thanks a lot again.<br>
<br>
Anirban<br>
<br>
On Fri, Dec 3, 2010 at 7:35 PM, Justin A.
Lemkul<<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>
wrote:<br>
<br>
<br>
<br>
Anirban Ghosh wrote:<br>
<br>
Hi ALL,<br>
<br>
Its a very basic question but still...<br>
When we calculate RMSD (or any other
parameter) using the g_rms<br>
command, we need to supply the .tpr file
with -s option. Now<br>
suppose if I have a total 20 ns simulation
with 4 breaks (i.e 5<br>
ns in each run), then there will be 4 .tpr
files. So at the end<br>
of 20 ns if I wish to calculate RMSD, then
which .tpr file<br>
should I suppy to g_rms, the first one or
the last one? We I run<br>
g_rms with the two .tpr files, I get
different results. So which<br>
one should be used? Any suggestion is
welcome.<br>
<br>
<br>
Use the one that contains the structure you
wish to serve as your<br>
reference.<br>
<br>
-Justin<br>
<br>
<br>
Thanks,<br>
<br>
Anirban<br>
<br>
<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><<a
moz-do-not-send="true" href="http://vt.edu"
target="_blank">http://vt.edu</a>> | (540)
231-9080<br>
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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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</blockquote>
--<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> |
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