<div dir="ltr">Hello all,<div><br></div><div>I am trying to run classical simulations with rigid 4 site polarisable water molecules using FIST. My simulation box contains water molecules and Na, Cl ions. When I try to restart a simulation I encounter the following error,</div><div><br></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">A constra</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">nt has been def</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">ned for a molecule type</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">    </span>| <span class="gmail-Apple-converted-space">  </span>but the atoms spec</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">f</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">ed </span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">n the constra</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">nt and the atoms def</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">ned for</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">    </span>| <span class="gmail-Apple-converted-space">  </span>the molecule DO NOT match!</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">    </span>|<span class="gmail-Apple-converted-space">  </span>Th</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">s could be very probable due to a wrong connect</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">v</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">ty, or an error</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">    </span>| <span class="gmail-Apple-converted-space">  </span></span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">n the constra</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">nt spec</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">f</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">cat</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">on </span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">n the </span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">nput f</span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">le.</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">    </span>| <span class="gmail-Apple-converted-space">  </span>Please check </span><span style="font-variant-ligatures:no-common-ligatures;background-color:rgb(224,228,9)">i</span><span style="font-variant-ligatures:no-common-ligatures">t carefully!</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">*******************************************************************************</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>* <span class="gmail-Apple-converted-space">  </span>___ <span class="gmail-Apple-converted-space">                                                                      </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>*<span class="gmail-Apple-converted-space">  </span>/ <span class="gmail-Apple-converted-space">  </span>\<span class="gmail-Apple-converted-space">                                                                      </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>* [ABORT] <span class="gmail-Apple-converted-space">                                                                    </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>*<span class="gmail-Apple-converted-space">  </span>\___/<span class="gmail-Apple-converted-space">                                                                      </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>*<span class="gmail-Apple-converted-space">    </span>|<span class="gmail-Apple-converted-space">                                                                        </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>*<span class="gmail-Apple-converted-space">  </span>O/|<span class="gmail-Apple-converted-space">                                                                        </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>* /| |<span class="gmail-Apple-converted-space">                                                                        </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>*******************************************************************************</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>* <span class="gmail-Apple-converted-space">  </span>___ <span class="gmail-Apple-converted-space">                                                                      </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>===== Routine Calling Stack =====</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">            </span>6 topology_constraint_pack_4</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">            </span>5 topology_constraint_pack</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">            </span>4 topology_control</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space">            </span>3 fist_init</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>*******************************************************************************</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>* /| |<span class="gmail-Apple-converted-space">                                                                        </span>*</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>* / \ <span class="gmail-Apple-converted-space">                                        </span>topology_constraint_util.F:1213 *</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">





















</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>*******************************************************************************</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">However, when I run a simulation with only water molecules, the simulations restart properly with the .restart file. Am I missing something here ?</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">I have attached an input file for Na,Cl,water simulations with this email.</span></p><div><br></div><div>Thank you in advance for your help/suggestions.</div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><font face="Arial, sans-serif"><span style="line-height:16.12px">With Regards,</span></font></div><div><font face="Arial, sans-serif">Rajorshi Chattopadhyay,</font></div><div><font face="Arial, sans-serif">PhD Researcher in Mineralogy/Crystallography,</font></div><div><font face="Arial, sans-serif"><span style="line-height:16.12px">Institut für Geologie und Mineralogie,</span></font></div><div><font face="Arial, sans-serif"><span style="line-height:16.12px">Universität zu Köln, Germany<br></span></font></div><div style="font-size:small"><br></div><div style="font-size:small"><span style="line-height:16.12px;font-size:12.8px"></span></div></div></div></div></div></div></div>

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