Difference between revisions of "Canavan Task 10 - Molecular Dynamics Simulations"
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===distances between periodic boundaries=== |
===distances between periodic boundaries=== |
Revision as of 16:47, 7 July 2012
Contents
Protocol
Further information and commands can be found in the protocol.
Wildtype 2O4H
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
The job run for 5h22:37.
energies
<figtable id="wt_energies">
Energy | Reference value | Average | Err.Est. | RMSD | Tot-Drift | Plot |
Temperature | 298 | 297.914 | 0.0072 | 1.38693 | -0.00042403 (K) | <figure id="wt_temp"></figure> |
Pressure | 1.0 (Berendsen barostat) | 1.00763 | 0.018 | 111.943 | -0.0713928 (bar) | <figure id="wt_pressure"></figure> |
Potential | -592161 | 55 | 721.947 | -252.112 (kJ/mol) | <figure id="wt_potential"></figure> | |
Total Energy | -485680 | 54 | 886.726 | -252.262 (kJ/mol) | <figure id="wt_tot_energy"><xr nolink id="wt_tot_energy"</figure> |
</figtable>
distances between periodic boundaries
The shortest periodic distance is 1.6456 (nm) at time 7675 (ps), between atoms 15 and 4507