Dear gmx-users, <div><br></div><div>I am trying to perform the Normal Mode Analysis of 24 kDa protein in water. Here is the .mdp file I am using:</div><div><br></div><div><div>integrator = nm</div><div>dt = 0.002 </div>
<div>nsteps = 10000 </div><div>emtol = 1 </div><div>nstcomm = 1 </div><div>nstxout = 0 </div>
<div>nstxtcout = 1000</div><div>nstvout = 0 </div><div>nstlog = 5000 </div><div>nstenergy = 20 </div><div>nstlist = 6 </div>
<div>ns_type = grid </div><div>coulombtype = cut-off</div><div>epsilon_r = 80.0</div><div>rcoulomb = 1.4</div><div>fourierspacing = 0.12</div><div>pmeorder = 4</div>
<div>optimize_fft = yes</div><div>ewald_rtol = 1.0e-5</div><div>DispCorr = EnerPres</div><div>constraints = none</div><div>rlist = 0.9 </div><div>rvdw = 0.9 </div>
<div>Tcoupl = berendsen </div><div>ref_t<span class="Apple-tab-span" style="white-space:pre">                </span> = 330 </div><div>tc-grps = protein<span class="Apple-tab-span" style="white-space:pre">                        </span></div>
<div>tau_t<span class="Apple-tab-span" style="white-space:pre">                </span> = 0.5 </div><div>Pcoupl = no <span class="Apple-tab-span" style="white-space:pre">        </span></div><div>Pcoupltype = isotropic </div>
<div>tau_p = 1.0 </div><div>compressibility = 4.5e-5</div><div>ref_p = 1.0</div><div>gen_vel = no </div><div>gen_temp = 300 </div>
<div>gen_seed = 1993 </div></div><div><br></div><div><br></div><div>And I get the error message: </div><div><br></div><div><div>Fatal error:</div><div>Constraints present with Normal Mode Analysis, this combination is not supported</div>
<div>For more information and tips for troubleshooting, please check the GROMACS</div><div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div><div><br></div>
<div>despite the constraint = none line. </div><div><br></div><div>I am using GROMACS 4.5.4</div><div><br></div><div>Any suggestions will be very welcomed</div><div><br></div><div>Thanks!</div><div><br></div><div><br></div>
-- <br>Andrey Dyachenko<br>PhD Student<div><br></div><div>Design, structure and synthesis of peptides and proteins<br>Institute for Research in Biomedicine (IRB Barcelona)<br>C/Baldiri i Reixac 10-12<br>08028 Barcelona<br>
Tel: +34 93 403 71 27<br>Fax: +34 93 403 71 26<br><a href="http://www.irbbarcelona.org" target="_blank">www.irbbarcelona.org</a><br><a href="http://www.pcb.ub.es/giralt/html/home.html" target="_blank">www.pcb.ub.es/giralt/html/home.html</a></div>
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