[gmx-users] Re: change in the secondary structure after simulation

bharat gupta bharat.85.monu at gmail.com
Thu Jan 27 08:45:57 CET 2011

I actually don't understand exactly what u are asking .. since I am not an
expert with gromacs..

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

          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

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
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