Sir, <br><br> I am extremely sorry for this question again :(<br>but I wanted to know this violation exists only in <br>first 50ns but after that even though there appears<br>to be a point of violation its only 1.39nm which is <br>
o0.01nm less than the cut off which I hope does <br>not cause serious trouble (as the minimum bond <br>length is of the order of 1 Angs) So can I make use <br>of this part of trajectory? <br><br> I know that this part of the trajectory have been <br>
arrived at through flawed interactions. But have any one<br>made such an attempt to analyze this?<br><br>Sorry again!<br><br>With regards<br>M. Kavyashree<br><br><div class="gmail_quote">On Tue, Jun 21, 2011 at 2:46 AM, Justin A. Lemkul <span dir="ltr"><<a 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>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear users,<br>
I ran 100ns simulation for 4 proteins, 3 of them were<br>
non covalent dimers in solution, but only 1 is a covalent<br>
dimer connected by a disulphide bridge. I used monomers<br>
to run the job.<br>
Only in the case of covalent dimer I was getting severe<br>
minimum image violation ie. out of 50001 data points,<br>
282 are <= 1.4nm<br>
280 are < 1.4nm<br>
144 are < 1.3nm<br>
79 are < 1.2nm<br>
28 are < 1.1nm<br>
4 < 1.0nm<br>
<br>
I agree that this is quite wrong but I wanted to know whether<br>
any useful information can be gathered out of this simulation?<br>
<br>
</blockquote>
<br></div>
Not likely. Nearly 2% of the saved frames are unusable, indicating that potentially even more of the frames in the trajectory are useless, as well, and the dynamics that produced them are flawed.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
In another data while calculating the energy terms it gives<br>
nan (not a number error) for rmsd alone eg -<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
------------------------------<u></u>------------------------------<u></u>-------------------<br>
Temperature 300 9e-05 -nan -0.000501989 (K)<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
------------------------------<u></u>------------------------------<u></u>-------------------<br>
Pressure 0.99914 0.027 -nan 0.0174391 (bar)<br>
<br>
Energy Average Err.Est. RMSD Tot-Drift<br>
------------------------------<u></u>------------------------------<u></u>-------------------<br>
Volume 517.755 0.0094 -nan 0.010871 (nm^3)<br>
Initially i though some data points are missing but later<br>
gmxcheck gives that all the data points are present.<br>
now what could be the error?<br>
<br>
I had asked this question before and was instructed to check the<br>
trajectory. I checked the rmsd rmsf of this with the other proteins<br>
it similar but one of the segment has high rmsf compared to the other<br>
proteins.<br>
<br>
</blockquote>
<br></div>
My advice to you was to *watch* the trajectory to see where the PBC violations occurred, not run more analysis. I doubt RMSF and RMSD will tell you anything useful.<br>
<br>
No one's been able to diagnose the problem based on this (continually posted) information. If it's a useless trajectory, why bother?<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanking you<br>
With regards<br>
M. Kavyashree<br>
<br>
<br>
<br>
</blockquote>
<br></div>
-- <br>
==============================<u></u>==========<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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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