Difference between revisions of "Canavan Task 10 - Molecular Dynamics Simulations"

From Bioinformatikpedia
(energies)
Line 61: Line 61:
 
-------------------------------------------------------------------------------
 
-------------------------------------------------------------------------------
 
Total Energy -485680 54 886.726 -252.262 (kJ/mol)
 
Total Energy -485680 54 886.726 -252.262 (kJ/mol)
  +
  +
  +
===distances between periodic boundaries===
  +
  +
The shortest periodic distance is 1.6456 (nm) at time 7675 (ps),
  +
between atoms 15 and 4507

Revision as of 17:51, 4 July 2012

Protocol

Further information can be found in the protocol.

Wildtype 2O4H

The commands can be found in the protocol.

gmxcheck

There are 2000 time frames, with a resolution of 5 psec. Therefore the whole simulation ran for 10000 psec = 10 nsec.


There are several atoms outside of the box.

atom# name  residue r_vdw  coordinate
  406  HE1  HIS  23 0.04     5.3   8.72   2.92
  408  HE2  HIS  23 0.04    5.47   8.69   2.73
  480  HB1  ASN  27 0.04    5.14   8.67   2.39
  482   CG  ASN  27 0.15    5.32    8.7   2.29
  483  OD1  ASN  27 0.105   5.32    8.7   2.17
  484  ND2  ASN  27 0.11    5.41   8.79   2.35
  485 HD21  ASN  27 0.04    5.41   8.79   2.45
  486 HD22  ASN  27 0.04    5.47   8.84   2.29
  500 MCB1  ALA  29 0       5.68   8.69   1.97
  501 MCB2  ALA  29 0       5.63   8.68   2.05

log file

energies

Convergence of energies can be observed.

Temperature

reference temperature from _md.mdp: 298K (thermostat:v-rescale)

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Temperature                 297.914     0.0072    1.38693 -0.00042403  (K)


Pressure:

reference pressure from _md.mdp: 1.0 (Berendsen barostat)

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                    1.00763      0.018    111.943 -0.0713928  (bar)


Potential:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Potential                   -592161         55    721.947   -252.112  (kJ/mol)


Total energy:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Total Energy                -485680         54    886.726   -252.262  (kJ/mol)


distances between periodic boundaries

The shortest periodic distance is 1.6456 (nm) at time 7675 (ps), between atoms 15 and 4507