hello sir,<br>i am following lysozyme tutorial for my dynamics.<br>when i go for equilibration first we need to do NVT. there i set 300K ...<br>At the end of NVT when i check my temperature using my edr file i am not getting equilbrium temp..<br>
it showed 239K  one time and sometime 329K like this..but not around 300K..<br>then when i changed my time (by changing number of steps)also i am not getting equilibrium temp.<br><br>how can i attain equilibrium..<br>pls help me with your answer..<br>
<br>This is my nvt.mdp file<br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CMD%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><style>
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<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">title<span style>           </span>=GROMOS43a1 lipopeptide NVT
equilibration</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">define<span style>          </span>= -DPOSRES<span style>      </span>; position restrain the protein</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">; Run parameters</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">integrator<span style>      </span>= md<span style>            </span>; leap-frog integrator</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">nsteps<span style>          </span>= 100000<span style>                </span>; 2 * 100000 = 200 ps</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">dt<span style>              </span>= 0.002<span style>         </span>; 2 fs</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">; Output
control</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">nstxout<span style>         </span>= 100<span style>           </span>; save coordinates every 0.2 ps</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">nstvout<span style>   </span><span style>      </span>= 100<span style>           </span>; save velocities every 0.2 ps</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">nstenergy<span style>       </span>= 100<span style>           </span>; save energies every 0.2 ps</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">nstlog<span style>          </span>= 100<span style>           </span>; update log file every 0.2 ps</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">; Bond
parameters</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">continuation<span style>    </span>= no<span style>            </span>; first dynamics run</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">constraint_algorithm
= lincs<span style>    </span>; holonomic constraints</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">constraints<span style>     </span>= all-bonds<span style>     </span>; all bonds (even heavy atom-H bonds)
constrained</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">lincs_iter<span style>      </span>= 1<span style>    
</span>; accuracy of LINCS</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">lincs_order<span style>     </span>= 4<span style>             </span>; also related to accuracy</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">;
Neighborsearching</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">ns_type<span style>         </span>= grid<span style>          </span>; search neighboring grid cells</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">nstlist<span style>         </span>= 5<span style>             </span>; 10 fs</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">rlist<span style>           </span>= 1.0<span style>           </span>; short-range neighborlist cutoff
(in nm)</span></p>

<p class="MsoNormal" style><span style="font-size:10pt;font-family:Arial">rcoulomb<span style>        </span>= 1.0<span style>           </span>; short-range electrostatic cutoff
(in nm)</span></p>

<br><br><br>Is it correct if i proceed with that wrong temperature file..<br><br>Thanking you,<br>