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>> wrote:
Mark Abraham wrote:
On 01/27/11, *bharat gupta * <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>>
--
========================================
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>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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