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><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 href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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">On 14/05/2011 10:52 PM, XAvier Periole wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
On May 14, 2011, at 1:11 PM, Justin A. Lemkul wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
Ramachandran G wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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>
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========================================<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><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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