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On 27/01/2011 11:11 PM, bharat gupta wrote:
<blockquote
cite="mid:AANLkTinspbg8oYJ8KOsVXLHTkaZ-yjkasKmqfGo6Jiz9@mail.gmail.com"
type="cite">
<div>I used the same .mdp files that are given in the lysozyme
tutorial .. Since I was knowing what all parameters to change ..
but after energy minimization and equilibration steps , the
graphs that I got were fine ... even the rmsd graph of the final
structure is also fine .. I have attached the final rmsd graph
of the structure .. </div>
</blockquote>
<br>
That suggests the problem was in the structure you started the
simulation from, like I've suggested a few times now :-)<br>
<br>
Mark<br>
<blockquote
cite="mid:AANLkTinspbg8oYJ8KOsVXLHTkaZ-yjkasKmqfGo6Jiz9@mail.gmail.com"
type="cite">
<div class="gmail_quote">On Thu, Jan 27, 2011 at 3:44 AM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">
<div><br>
<br>
bharat gupta wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204,
204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">I generated the secondary structure
profile of structure retrieved from the last frame of the
simulation ... In that profile those amino acids that are
shown as loops in VMD doesnot have any secondary structure
assignment ... it means that during simulation the
structure got changed some how ... and It's really
surprising ?? ... Can u tell me where can the fault be as
I am planning to do the simulation again and this time I
will check the structure after every step .. but for that
I want to know how can I save the structure after every
step say for eg. after energy minimization ..<br>
<br>
</blockquote>
<br>
</div>
Secondary structure is dependent upon the chosen force field
and the .mdp settings. Since you've posted neither, there's
no way to tell what might be to blame.<br>
<br>
You can save more frequently by setting the proper output
controls. Read in the manual about the nst* options and set
the accordingly.<br>
<br>
-Justin<br>
<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204);
margin: 0px 0px 0px 0.8ex; padding-left: 1ex;"
class="gmail_quote">
<div>On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a> <mailto:<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Mark Abraham wrote:<br>
<br>
<br>
<br>
On 01/27/11, *bharat gupta * <<a
moz-do-not-send="true"
href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a><br>
</div>
<div>
<div> <mailto:<a moz-do-not-send="true"
href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>>>
wrote:<br>
<br>
I actually don't understand exactly what u
are asking ..<br>
since I am not an expert with gromacs..<br>
<br>
<br>
Please leave the old context for the discussion
in future<br>
emails. Only you are paying so much attention to
your work that<br>
you can be sure of remembering things :-)<br>
<br>
If your simulation started with these strands
unfolded, then<br>
your problem is somewhere else. However, you have
to be able to<br>
tell us what was the initial conformation, and
when your "first<br>
trajectory frame" (per last email) happened in
the simulation.<br>
<br>
<br>
I would also add that VMD does a fairly poor job
sometimes of<br>
guessing secondary structure. So if no beta strand
was present in<br>
the very first frame, that doesn't necessarily mean
the secondary<br>
structure wasn't stable, it just means VMD didn't
display it properly.<br>
<br>
-Justin<br>
<br>
Mark<br>
<br>
<br>
I don't know when is was written .. Here are
some lines from<br>
the log files of simulation ...<br>
Statistics over 1500001 steps using 300001
frames<br>
<br>
Energies (kJ/mol)<br>
Angle Proper Dih. Ryckaert-Bell.
LJ-14<br>
Coulomb-14<br>
7.35090e+03 4.37413e+02 3.60104e+03
5.26705e+03<br>
2.58894e+04<br>
LJ (SR) Disper. corr. Coulomb (SR)
Coul. recip.<br>
Potential<br>
1.05399e+05 -2.92853e+03 -6.79288e+05
-1.07015e+05<br>
-6.41286e+05<br>
Kinetic En. Total Energy Temperature
Pres. DC (bar)<br>
Pressure (bar)<br>
1.03484e+05 -5.37802e+05 3.00003e+02
-2.37485e+02<br>
1.02890e+00<br>
Constr. rmsd<br>
0.00000e+00<br>
<br>
Box-X Box-Y Box-Z<br>
7.42618e+00 7.42618e+00 7.42618e+00<br>
<br>
Total Virial (kJ/mol)<br>
3.44183e+04 3.40020e+01 -1.17357e+01<br>
3.42160e+01 3.45369e+04 -2.46337e+01<br>
-1.16644e+01 -2.48479e+01 3.44949e+04<br>
<br>
Pressure (bar)<br>
1.99809e+00 9.48448e-02 4.57909e-01<br>
7.74354e-02 4.97824e-01 1.84797e+00<br>
4.52125e-01 1.86535e+00 5.90776e-01<br>
<br>
Total Dipole (D)<br>
-1.86272e+02 4.46310e+01 2.08554e+02<br>
<br>
T-Protein T-non-Protein<br>
2.99904e+02 3.00013e+02<br>
<br>
<br>
M E G A - F L O P S A C C O U N T I N G<br>
<br>
<br>
There were in total 1502 frames (as shown in
VMD )...<br>
I don't know about how it compared with the
coordinates of<br>
the structure that I gave to grompp<br>
<br>
--------<br>
<br>
Pls guide<br>
<br>
<br>
<br>
<br>
-- Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer
Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680,
+82-51-583-8343<br>
Mobile no. - 010-5818-3680<br>
E-mail : <a moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>
<mailto:<a moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>><br>
</div>
</div>
<mailto:<a moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>
<mailto:<a moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a>>>
<div><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>
</div>
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<br>
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
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</blockquote>
<div>
<div><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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<br>
<br clear="all">
<br>
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343
<div>Mobile no. - 010-5818-3680<br>
E-mail : <a moz-do-not-send="true"
href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
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