Mark Abraham wrote:
On 01/27/11, *bharat gupta * <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>
--
========================================
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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