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On 15/05/2011 12:01 AM, Sikandar Mashayak wrote:
<blockquote
cite="mid:BANLkTi=q7Wo7NSwW7jasLEq0N=KHMdTseA@mail.gmail.com"
type="cite">Hey Mark
<div><br>
</div>
<div>Do you mean removing all bond definitions from topology file,
when you say well constructed topology to exclude all
bonded-interactions in rerun?</div>
</blockquote>
<br>
I said you can decompose the bonded interactions. You can have none
by removing all bonded interactions, but that won't save you any
significant time, nor serve any other purpose.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=q7Wo7NSwW7jasLEq0N=KHMdTseA@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>thanks</div>
<div>sikandar</div>
<div><br>
<div class="gmail_quote">On Sat, May 14, 2011 at 8:01 AM, 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>
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padding-left: 1ex;">
<div class="im">On 14/05/2011 10:52 PM, XAvier Periole
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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padding-left: 1ex;">
<br>
Two things you have to be careful about:<br>
1- use trr trajectory files. xtc precision is not
sufficient and it will give a lot of discrepancies at
least for the bonded terms.<br>
2- set the nstlist to 1 as the neiboring list should be
undated for each frame and not every 5/10 as it is
normally set in a regular mdp file.<br>
</blockquote>
<br>
</div>
Reruns do neighbour searching every frame, regardless.<br>
<font color="#888888">
<br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
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<br>
On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote:<br>
<br>
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204); padding-left: 1ex;">
<br>
<br>
Ramachandran G wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt
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204, 204); padding-left: 1ex;">
Hello gmx users:<br>
I did 1ns simulation for my system and have
the trajectory and energy files.<br>
Now i want to see the energy of some specific
residues. So, i decompose(separated) the energy
groups and edited the mdp file.<br>
Using the mdp file, i created a new tpr file and
rerun the mdrun using the trajectory file. But
when i compared the total energy between the old
and new one, it differs a lot.<br>
I am doing some mistakes somewhere. Can anyone
help me please. Thanks.<br>
</blockquote>
<br>
Maybe, maybe not. Without seeing the .mdp settings
and the data that you're looking at, all anyone can
do is guess. You also haven't stated what type of
trajectory (i.e. .xtc or .trr) you're using as
-rerun input. If you're using an .xtc file, there
is no velocity information, so any property related
to velocities (most notably kinetic energy, but
several others as well) will be zero. I suspect
this is probably where the discrepancy is, but it is
not a problem. Using energygrps is only useful for
decomposing short-range nonbonded energy terms,
nothing else.<br>
<br>
-Justin<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="tel:%28540%29%20231-9080"
value="+15402319080" target="_blank">(540)
231-9080</a><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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