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

From Bioinformatikpedia
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===energies===
 
===energies===
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For all analysed thermodynamical parameters convergence could be observed. Though, for pressure the values vary enormously, but the average pressure is close to the specified value of 1 bar.
   
 
<figtable id="wt_energies">
 
<figtable id="wt_energies">
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<td>1.38693</td>
 
<td>1.38693</td>
 
<td>-0.00042403 (K)</td>
 
<td>-0.00042403 (K)</td>
<td><figure id="wt_temp">[[File:wt_temp.png|thumb|300px|<b><xr nolink id="wt_temp"/></b></br>]]</figure></td>
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<td><figure id="wt_temp">[[File:wt_temp.png|thumb|200px|<b><xr nolink id="wt_temp"/></b></br>]]</figure></td>
 
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<td>111.943</td>
 
<td>111.943</td>
 
<td>-0.0713928 (bar)</td>
 
<td>-0.0713928 (bar)</td>
<td><figure id="wt_pressure">[[File:CD_wt_pressure.png|thumb|300px|<b><xr nolink id="wt_pressure"/></b></br>]]</figure></td>
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<td><figure id="wt_pressure">[[File:CD_wt_pressure.png|thumb|200px|<b><xr nolink id="wt_pressure"/></b></br>]]</figure></td>
 
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<td>721.947</td>
 
<td>721.947</td>
 
<td>-252.112 (kJ/mol)</td>
 
<td>-252.112 (kJ/mol)</td>
<td><figure id="wt_potential">[[File:CD_wt_potential.png|thumb|300px|<b><xr nolink id="wt_potential"/></b></br>]]</figure></td>
+
<td><figure id="wt_potential">[[File:CD_wt_potential.png|thumb|200px|<b><xr nolink id="wt_potential"/></b></br>]]</figure></td>
 
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<td>886.726</td>
 
<td>886.726</td>
 
<td>-252.262 (kJ/mol)</td>
 
<td>-252.262 (kJ/mol)</td>
<td><figure id="wt_tot_energy">[[File:CD_wt_tot_energy.png|thumb|300px|<b><xr nolink id="wt_tot_energy"/></b></br>]]</figure></td>
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<td><figure id="wt_tot_energy">[[File:CD_wt_tot_energy.png|thumb|200px|<b><xr nolink id="wt_tot_energy"/></b></br>]]</figure></td>
 
</tr>
 
</tr>
   

Revision as of 16:56, 7 July 2012

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

For all analysed thermodynamical parameters convergence could be observed. Though, for pressure the values vary enormously, but the average pressure is close to the specified value of 1 bar.

<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">
<xr nolink id="wt_temp"/>
</figure>
Pressure 1.0 (Berendsen barostat) 1.00763 0.018 111.943 -0.0713928 (bar) <figure id="wt_pressure">
<xr nolink id="wt_pressure"/>
</figure>
Potential -592161 55 721.947 -252.112 (kJ/mol) <figure id="wt_potential">
<xr nolink 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