On Thu, Jan 27, 2011 at 3:44 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
bharat gupta wrote:
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 ..
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.
You can save more frequently by setting the proper output
controls. Read in the manual about the nst* options and set
the accordingly.
-Justin
On Thu, Jan 27, 2011 at 8:35 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
Mark Abraham wrote:
On 01/27/11, *bharat gupta *
<bharat.85.m...@gmail.com <mailto:bharat.85.m...@gmail.com>
<mailto:bharat.85.m...@gmail.com
<mailto:bharat.85.m...@gmail.com>>> wrote:
I actually don't understand exactly what u are
asking ..
since I am not an expert with gromacs..
Please leave the old context for the discussion in
future
emails. Only you are paying so much attention to
your work that
you can be sure of remembering things :-)
If your simulation started with these strands
unfolded, then
your problem is somewhere else. However, you have
to be able to
tell us what was the initial conformation, and when
your "first
trajectory frame" (per last email) happened in the
simulation.
I would also add that VMD does a fairly poor job
sometimes of
guessing secondary structure. So if no beta strand was
present in
the very first frame, that doesn't necessarily mean the
secondary
structure wasn't stable, it just means VMD didn't
display it properly.
-Justin
Mark
I don't know when is was written .. Here are
some lines from
the log files of simulation ...
Statistics over 1500001 steps using 300001 frames
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell.
LJ-14
Coulomb-14
7.35090e+03 4.37413e+02 3.60104e+03
5.26705e+03
2.58894e+04
LJ (SR) Disper. corr. Coulomb (SR)
Coul. recip.
Potential
1.05399e+05 -2.92853e+03 -6.79288e+05
-1.07015e+05
-6.41286e+05
Kinetic En. Total Energy Temperature
Pres. DC (bar)
Pressure (bar)
1.03484e+05 -5.37802e+05 3.00003e+02
-2.37485e+02
1.02890e+00
Constr. rmsd
0.00000e+00
Box-X Box-Y Box-Z
7.42618e+00 7.42618e+00 7.42618e+00
Total Virial (kJ/mol)
3.44183e+04 3.40020e+01 -1.17357e+01
3.42160e+01 3.45369e+04 -2.46337e+01
-1.16644e+01 -2.48479e+01 3.44949e+04
Pressure (bar)
1.99809e+00 9.48448e-02 4.57909e-01
7.74354e-02 4.97824e-01 1.84797e+00
4.52125e-01 1.86535e+00 5.90776e-01
Total Dipole (D)
-1.86272e+02 4.46310e+01 2.08554e+02
T-Protein T-non-Protein
2.99904e+02 3.00013e+02
M E G A - F L O P S A C C O U N T I N G
There were in total 1502 frames (as shown in
VMD )...
I don't know about how it compared with the
coordinates of
the structure that I gave to grompp
--------
Pls guide
-- Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer
Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
<mailto:monu46...@yahoo.com> <mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>>
<mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com> <mailto:monu46...@yahoo.com
<mailto:monu46...@yahoo.com>>>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu
<http://vt.edu/>> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
<mailto:monu46...@yahoo.com <mailto:monu46...@yahoo.com>>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
