<div dir="ltr">Dear Sumit Agrawal,<div><br></div><div>I suggest the Packmol software to construct initial configurations, It is a simple and tractable, where you can decide where put some particular molecules, the siz of the box, the number of different molecules, and there is a criteria to ensure your molecules are not so near between them. For little boxes is useful, but for big systems is mandatory to use a program like Packmol.</div><div><a href="http://m3g.iqm.unicamp.br/packmol/home.shtml">http://m3g.iqm.unicamp.br/packmol/home.shtml</a><br></div><div><br></div><div><br></div><div>Regards</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El vie., 16 oct. 2020 a las 14:20, Vasyl Stotskyi (<<a href="mailto:vasyl....@gmail.com">vasyl....@gmail.com</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Dear Sumit Agrawal,</div><div>Sure, if you can save it in one of avogadro readable formats (.xyz, .cif, ....). </div><div>If initial geometries of molecules in gaus view will be fine, then you don't have to optimize it in Avogadro, i.e. if you will not have O-H bonds with more than 1.5 angstrom length or overlap of molecules, or huge vacuum between molecules. Avogadro optimization is the most useful only for such bad cases.</div><div>Best regards,</div><div>Vasyl</div><br><div>On Oct 17 2020, at 12:40 am, sumit agrawal <<a href="mailto:sumitag...@gmail.com" target="_blank">sumitag...@gmail.com</a>> wrote:</div><blockquote><div><div>Dear Vasyl,</div><div><br></div><div>Thanks for the answer. So I have to manually draw 100 molecules of water and methanol in Avogadro? Actually, I am more comfortable with gauss views. So can i make a coordinate file in gusse view then pre optimize in the avogadro ? </div><div><br></div></div><br><img alt="Sent from Mailspring" width="0" height="0" style="border: 0px; width: 0px; height: 0px;" src="https://link.getmailspring.com/open/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE@getmailspring.com?me=0f52c36e&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t"><div class="gmail_quote"><div class="gmail_attr"><div>On Fri, Oct 16, 2020 at 9:04 AM Vasyl Stotskyi <<a href="mailto:vasyl....@gmail.com" title="mailto:vasyl....@gmail.com" target="_blank">vasyl....@gmail.com</a>> wrote:</div></div><blockquote><div>Dear Sumit Agrawal,</div><div>You can create some model in Avogadro. There you can pre-optimize it with force fields, and save as .xyz file. In CP2K, then you can read coordinates from .xyz file. Please, read manual for this (<a href="https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/0?redirect=https%3A%2F%2Fmanual.cp2k.org%2Fcp2k-7_1-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2FTOPOLOGY.html&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" title="https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/0?redirect=https%3A%2F%2Fmanual.cp2k.org%2Fcp2k-7_1-branch%2FCP2K_INPUT%2FFORCE_EVAL%2FSUBSYS%2FTOPOLOGY.html&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" target="_blank">https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY.html</a>).</div><div>Best regards,</div><div>Vasyl</div><div>On Oct 16 2020, at 11:27 pm, sumit agrawal <<a href="mailto:sumitag...@gmail.com" title="mailto:sumitag...@gmail.com" target="_blank">sumitag...@gmail.com</a>> wrote:</div><blockquote><div><div>Hii,</div><div><br></div><div>I have recently installed cp2k in windows. I just did some exercise which is available on cp2k website. Now I want to do some bulk phase vibrational analysis. I want to make a coordinate file in which 100 water molecules and one methanol molecule is present. This methanol molecule is present in between water molecules. So how to make a coordinate file for this system.</div><div><br></div><div>Can I use gauss view to make the coordinate file?</div></div><br><div>--</div><div>You received this message because you are subscribed to the Google Groups "cp2k" group.</div><div>To unsubscribe from this group and stop receiving emails from it, send an email to <a href="https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/1?redirect=mailto%3Acp2k%2Bunsubscribe%40googlegroups.com&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" title="https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/1?redirect=mailto%3Acp2k%2Bunsubscribe%40googlegroups.com&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" target="_blank">cp...@googlegroups.com</a>.</div><div>To view this discussion on the web visit <a href="https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/2?redirect=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fcp2k%2FCALSDoYad_FGm4Qh5SRvZcMun3fe%253D5q1xpxeW3T5SoMcAoTH52A%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" title="https://link.getmailspring.com/link/FC05854F-A2E3-45BD-9677-A12F225F42A8@getmailspring.com/2?redirect=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fcp2k%2FCALSDoYad_FGm4Qh5SRvZcMun3fe%253D5q1xpxeW3T5SoMcAoTH52A%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" target="_blank">https://groups.google.com/d/msgid/cp2k/CALSDoYad_FGm4Qh5SRvZcMun3fe%3D5q1xpxeW3T5SoMcAoTH52A%40mail.gmail.com</a>.</div></blockquote><br><div>--</div><div>You received this message because you are subscribed to the Google Groups "cp2k" group.</div><div>To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp...@googlegroups.com" title="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.</div><div>To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/FC05854F-A2E3-45BD-9677-A12F225F42A8%40getmailspring.com?utm_medium=email&utm_source=footer" title="https://groups.google.com/d/msgid/cp2k/FC05854F-A2E3-45BD-9677-A12F225F42A8%40getmailspring.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/FC05854F-A2E3-45BD-9677-A12F225F42A8%40getmailspring.com</a>.</div></blockquote></div><br><div>--</div><div>You received this message because you are subscribed to the Google Groups "cp2k" group.</div><div>To unsubscribe from this group and stop receiving emails from it, send an email to <a href="https://link.getmailspring.com/link/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE@getmailspring.com/0?redirect=mailto%3Acp2k%2Bunsubscribe%40googlegroups.com&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" title="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.</div><div>To view this discussion on the web visit <a href="https://link.getmailspring.com/link/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE@getmailspring.com/1?redirect=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fcp2k%2FCALSDoYaSwE%253DyxwswTkq6U5OouRZPiuev3yRJDydn%252B37kF-G4%252Bg%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter&recipient=Y3Aya0Bnb29nbGVncm91cHMuY29t" title="https://groups.google.com/d/msgid/cp2k/CALSDoYaSwE%3DyxwswTkq6U5OouRZPiuev3yRJDydn%2B37kF-G4%2Bg%40mail.gmail.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/CALSDoYaSwE%3DyxwswTkq6U5OouRZPiuev3yRJDydn%2B37kF-G4%2Bg%40mail.gmail.com</a>.</div></blockquote> <p></p> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE%40getmailspring.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/E1FD0EA3-5F69-4894-B38E-7FA74A2088EE%40getmailspring.com</a>.<br> </blockquote></div>