Please keep gmx-users correspondence on the mailing list, so that others can learn from and contribute to the discussion and/or archives.<br /><br /><span>On 19/07/11, <b class="name">&quot;Marzinek, Jan&quot; </b> &lt;j.marzinek10@imperial.ac.uk&gt; wrote:</span><blockquote cite="mid:787E9EFEEFC7384580812E4CA26D4F4405227E@icexch-m4.ic.ac.uk" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span xmlns="http://www.w3.org/TR/REC-html40" xmlns:a="urn:schemas-microsoft-com:office:access" xmlns:b="urn:schemas-microsoft-com:office:publisher" xmlns:c="urn:schemas-microsoft-com:office:component:spreadsheet" xmlns:d="DAV:" xmlns:dir="http://schemas.microsoft.com/sharepoint/soap/directory/" xmlns:ds="http://www.w3.org/2000/09/xmldsig#" xmlns:dsp="http://schemas.microsoft.com/sharepoint/dsp" xmlns:dssi="http://schemas.microsoft.com/office/2006/digsig" xmlns:dsss="http://schemas.microsoft.com/office/2006/digsig-setup" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:ec="http://www.w3.org/2001/04/xmlenc#" xmlns:ex12m="http://schemas.microsoft.com/exchange/services/2006/messages" xmlns:ex12t="http://schemas.microsoft.com/exchange/services/2006/types" xmlns:html="http://www.w3.org/TR/REC-html40" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:mdssi="http://schemas.openxmlformats.org/package/2006/digital-signature" xmlns:mrels="http://schemas.openxmlformats.org/package/2006/relationships" xmlns:mt="http://schemas.microsoft.com/sharepoint/soap/meetings/" xmlns:mver="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:oa="urn:schemas-microsoft-com:office:activation" xmlns:odc="urn:schemas-microsoft-com:office:odc" xmlns:ois="http://schemas.microsoft.com/sharepoint/soap/ois/" xmlns:p="urn:schemas-microsoft-com:office:powerpoint" xmlns:ppda="http://www.passport.com/NameSpace.xsd" xmlns:pptsl="http://schemas.microsoft.com/sharepoint/soap/SlideLibrary/" xmlns:q="http://schemas.xmlsoap.org/soap/envelope/" xmlns:repl="http://schemas.microsoft.com/repl/" xmlns:rs="urn:schemas-microsoft-com:rowset" xmlns:rtc="http://microsoft.com/officenet/conferencing" xmlns:s="uuid:BDC6E3F0-6DA3-11d1-A2A3-00AA00C14882" xmlns:sp="http://schemas.microsoft.com/sharepoint/" xmlns:sps="http://schemas.microsoft.com/sharepoint/soap/" xmlns:spsl="http://microsoft.com/webservices/SharePointPortalServer/PublishedLinksService" xmlns:spwp="http://microsoft.com/sharepoint/webpartpages" xmlns:ss="urn:schemas-microsoft-com:office:spreadsheet" xmlns:st="" xmlns:sub="http://schemas.microsoft.com/sharepoint/soap/2002/1/alerts/" xmlns:udc="http://schemas.microsoft.com/data/udc" xmlns:udcp2p="http://schemas.microsoft.com/data/udc/parttopart" xmlns:udcs="http://schemas.microsoft.com/data/udc/soap" xmlns:udcxf="http://schemas.microsoft.com/data/udc/xmlfile" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:wf="http://schemas.microsoft.com/sharepoint/soap/workflow/" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:x2="http://schemas.microsoft.com/office/excel/2003/xml" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:z="#RowsetSchema"><p>

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<p class="MsoNormal">On 19/07/11, <b>&quot;Marzinek, Jan&quot; </b>&lt;<a href="mailto:j.marzinek10@imperial.ac.uk">j.marzinek10@imperial.ac.uk</a>&gt; wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="">Dear Gromacs Users,<o:p></o:p></p>
<p class="MsoNormal" style=""> <o:p></o:p></p>
<p class="MsoNormal" style="">As I know for the Energy Minimization algorithms both Steepest Descent and Conjugate Gradient will not provide a global minimum of the potential energy but only a local minium.<o:p></o:p></p>
<p class="MsoNormal" style="">Does anyone know how Gromacs choose the starting point on the potential energy hypersurface for the beginning of Energy Minimization?
<o:p></o:p></p>
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You choose it with the starting configuration you provide to grompp.<br />
<br />
Mark<br />
<br />
<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: &quot;Calibri&quot;,&quot;sans-serif&quot;;">Hi,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size: 11pt; font-family: &quot;Calibri&quot;,&quot;sans-serif&quot;;">Thank you for your response. I understand that you start from the coordinates which you specify in your gro file -&gt; Input. But where Gromacs start on the potential energy
 surface as it has many local minima, maxima, saddle points. </span></p></div></td></tr></tbody></table></p></span></div></blockquote><br />GROMACS starts with the configuration you provide.<br /><br /><blockquote cite="mid:787E9EFEEFC7384580812E4CA26D4F4405227E@icexch-m4.ic.ac.uk" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span xmlns="http://www.w3.org/TR/REC-html40" xmlns:a="urn:schemas-microsoft-com:office:access" xmlns:b="urn:schemas-microsoft-com:office:publisher" xmlns:c="urn:schemas-microsoft-com:office:component:spreadsheet" xmlns:d="DAV:" xmlns:dir="http://schemas.microsoft.com/sharepoint/soap/directory/" xmlns:ds="http://www.w3.org/2000/09/xmldsig#" xmlns:dsp="http://schemas.microsoft.com/sharepoint/dsp" xmlns:dssi="http://schemas.microsoft.com/office/2006/digsig" xmlns:dsss="http://schemas.microsoft.com/office/2006/digsig-setup" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:ec="http://www.w3.org/2001/04/xmlenc#" xmlns:ex12m="http://schemas.microsoft.com/exchange/services/2006/messages" xmlns:ex12t="http://schemas.microsoft.com/exchange/services/2006/types" xmlns:html="http://www.w3.org/TR/REC-html40" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:mdssi="http://schemas.openxmlformats.org/package/2006/digital-signature" xmlns:mrels="http://schemas.openxmlformats.org/package/2006/relationships" xmlns:mt="http://schemas.microsoft.com/sharepoint/soap/meetings/" xmlns:mver="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:oa="urn:schemas-microsoft-com:office:activation" xmlns:odc="urn:schemas-microsoft-com:office:odc" xmlns:ois="http://schemas.microsoft.com/sharepoint/soap/ois/" xmlns:p="urn:schemas-microsoft-com:office:powerpoint" xmlns:ppda="http://www.passport.com/NameSpace.xsd" xmlns:pptsl="http://schemas.microsoft.com/sharepoint/soap/SlideLibrary/" xmlns:q="http://schemas.xmlsoap.org/soap/envelope/" xmlns:repl="http://schemas.microsoft.com/repl/" xmlns:rs="urn:schemas-microsoft-com:rowset" xmlns:rtc="http://microsoft.com/officenet/conferencing" xmlns:s="uuid:BDC6E3F0-6DA3-11d1-A2A3-00AA00C14882" xmlns:sp="http://schemas.microsoft.com/sharepoint/" xmlns:sps="http://schemas.microsoft.com/sharepoint/soap/" xmlns:spsl="http://microsoft.com/webservices/SharePointPortalServer/PublishedLinksService" xmlns:spwp="http://microsoft.com/sharepoint/webpartpages" xmlns:ss="urn:schemas-microsoft-com:office:spreadsheet" xmlns:st="" xmlns:sub="http://schemas.microsoft.com/sharepoint/soap/2002/1/alerts/" xmlns:udc="http://schemas.microsoft.com/data/udc" xmlns:udcp2p="http://schemas.microsoft.com/data/udc/parttopart" xmlns:udcs="http://schemas.microsoft.com/data/udc/soap" xmlns:udcxf="http://schemas.microsoft.com/data/udc/xmlfile" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:wf="http://schemas.microsoft.com/sharepoint/soap/workflow/" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:x2="http://schemas.microsoft.com/office/excel/2003/xml" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:z="#RowsetSchema"><p><table><tbody><tr><td lang="EN-GB" link="blue" vlink="purple"><div class="WordSection1"><p class="MsoNormal"><span style="font-size: 11pt; font-family: &quot;Calibri&quot;,&quot;sans-serif&quot;;">Will it always go to the closest local minimum which is not global minimum?</span></p></div></td></tr></tbody></table></p></span></div></blockquote><br />Various optimization algorithms can be chosen in the .mdp file. Those algorithms are deterministic, but their properties vary. They will find a nearby local minimum eventually, but not necessarily the same one, or in a given number of steps. See manual or http://en.wikipedia.org/wiki/Energy_minimization<br /><br />Mark<blockquote cite="mid:787E9EFEEFC7384580812E4CA26D4F4405227E@icexch-m4.ic.ac.uk" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><span xmlns="http://www.w3.org/TR/REC-html40" xmlns:a="urn:schemas-microsoft-com:office:access" xmlns:b="urn:schemas-microsoft-com:office:publisher" xmlns:c="urn:schemas-microsoft-com:office:component:spreadsheet" xmlns:d="DAV:" xmlns:dir="http://schemas.microsoft.com/sharepoint/soap/directory/" xmlns:ds="http://www.w3.org/2000/09/xmldsig#" xmlns:dsp="http://schemas.microsoft.com/sharepoint/dsp" xmlns:dssi="http://schemas.microsoft.com/office/2006/digsig" xmlns:dsss="http://schemas.microsoft.com/office/2006/digsig-setup" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:ec="http://www.w3.org/2001/04/xmlenc#" xmlns:ex12m="http://schemas.microsoft.com/exchange/services/2006/messages" xmlns:ex12t="http://schemas.microsoft.com/exchange/services/2006/types" xmlns:html="http://www.w3.org/TR/REC-html40" xmlns:m="http://schem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