<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:p="urn:schemas-microsoft-com:office:powerpoint" xmlns:a="urn:schemas-microsoft-com:office:access" xmlns:dt="uuid:C2F41010-65B3-11d1-A29F-00AA00C14882" xmlns:s="uuid:BDC6E3F0-6DA3-11d1-A2A3-00AA00C14882" xmlns:rs="urn:schemas-microsoft-com:rowset" xmlns:z="#RowsetSchema" xmlns:b="urn:schemas-microsoft-com:office:publisher" xmlns:ss="urn:schemas-microsoft-com:office:spreadsheet" xmlns:c="urn:schemas-microsoft-com:office:component:spreadsheet" xmlns:odc="urn:schemas-microsoft-com:office:odc" xmlns:oa="urn:schemas-microsoft-com:office:activation" xmlns:html="http://www.w3.org/TR/REC-html40" xmlns:q="http://schemas.xmlsoap.org/soap/envelope/" xmlns:rtc="http://microsoft.com/officenet/conferencing" xmlns:D="DAV:" xmlns:Repl="http://schemas.microsoft.com/repl/" xmlns:mt="http://schemas.microsoft.com/sharepoint/soap/meetings/" xmlns:x2="http://schemas.microsoft.com/office/excel/2003/xml" xmlns:ppda="http://www.passport.com/NameSpace.xsd" xmlns:ois="http://schemas.microsoft.com/sharepoint/soap/ois/" 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:udc="http://schemas.microsoft.com/data/udc" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:sub="http://schemas.microsoft.com/sharepoint/soap/2002/1/alerts/" xmlns:ec="http://www.w3.org/2001/04/xmlenc#" xmlns:sp="http://schemas.microsoft.com/sharepoint/" xmlns:sps="http://schemas.microsoft.com/sharepoint/soap/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:udcs="http://schemas.microsoft.com/data/udc/soap" xmlns:udcxf="http://schemas.microsoft.com/data/udc/xmlfile" xmlns:udcp2p="http://schemas.microsoft.com/data/udc/parttopart" xmlns:wf="http://schemas.microsoft.com/sharepoint/soap/workflow/" xmlns:dsss="http://schemas.microsoft.com/office/2006/digsig-setup" xmlns:dssi="http://schemas.microsoft.com/office/2006/digsig" xmlns:mdssi="http://schemas.openxmlformats.org/package/2006/digital-signature" xmlns:mver="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:mrels="http://schemas.openxmlformats.org/package/2006/relationships" xmlns:spwp="http://microsoft.com/sharepoint/webpartpages" xmlns:ex12t="http://schemas.microsoft.com/exchange/services/2006/types" xmlns:ex12m="http://schemas.microsoft.com/exchange/services/2006/messages" xmlns:pptsl="http://schemas.microsoft.com/sharepoint/soap/SlideLibrary/" xmlns:spsl="http://microsoft.com/webservices/SharePointPortalServer/PublishedLinksService" xmlns:Z="urn:schemas-microsoft-com:" xmlns:st="" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Dear Gromacs users,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I am working with version 4.5.3, using the opls-aa forcefield in an implicit solvent, all-vs-all setting:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>pdb2gmx -ter -ff oplsaa -water none -f file.pdb<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I am energy-minimizing structures in 3 stages (steep, cg and l-bfgs). The last stage is the following:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>grompp -f em3.mdp -p topol.top -c em2.gro -t em2.trr -o em3.tpr -po em3.mdout.mdp<o:p></o:p></p><p class=MsoNormal>mdrun -nice 0 -v -pd -deffnm em3<o:p></o:p></p><p class=MsoNormal>g_energy -s em3.tpr -f em3.edr -o em3.potential_energy.xvg <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>where the mdp file is:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>;;;;;;;;;;;;;;;;;;; em3.mdp ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<o:p></o:p></p><p class=MsoNormal>integrator = l-bfgs<o:p></o:p></p><p class=MsoNormal>nsteps = 50000<o:p></o:p></p><p class=MsoNormal>implicit_solvent = GBSA<o:p></o:p></p><p class=MsoNormal>gb_algorithm = Still <o:p></o:p></p><p class=MsoNormal>sa_algorithm = Ace-approximation <o:p></o:p></p><p class=MsoNormal>pbc = no<o:p></o:p></p><p class=MsoNormal>rgbradii = 0 <o:p></o:p></p><p class=MsoNormal>ns_type = simple<o:p></o:p></p><p class=MsoNormal>nstlist = 0<o:p></o:p></p><p class=MsoNormal>rlist = 0<o:p></o:p></p><p class=MsoNormal>coulombtype = cut-off<o:p></o:p></p><p class=MsoNormal>rcoulomb = 0<o:p></o:p></p><p class=MsoNormal>vdwtype = cut-off<o:p></o:p></p><p class=MsoNormal>rvdw = 0<o:p></o:p></p><p class=MsoNormal>nstcalcenergy = 1<o:p></o:p></p><p class=MsoNormal>nstenergy = 1000<o:p></o:p></p><p class=MsoNormal>emtol = 0 <o:p></o:p></p><p class=MsoNormal>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The last line in the em3.potential_energy.xvg file should give the (potential) energy of the minimized structure em3.gro .<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I wish also to compute the potential energy of .gro files in general, not necessarily obtained from a simulation. For that, I prepared a .mdp file for a degenerate energy minimization, having 0 steps, designed just to give the status of the file:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>;;;;;;;;;;;;;;;;;;; status.mdp ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<o:p></o:p></p><p class=MsoNormal>integrator = l-bfgs<o:p></o:p></p><p class=MsoNormal>nsteps = 0<o:p></o:p></p><p class=MsoNormal>implicit_solvent = GBSA<o:p></o:p></p><p class=MsoNormal>gb_algorithm = Still<o:p></o:p></p><p class=MsoNormal>sa_algorithm = Ace-approximation<o:p></o:p></p><p class=MsoNormal>pbc = no<o:p></o:p></p><p class=MsoNormal>rgbradii = 0<o:p></o:p></p><p class=MsoNormal>ns_type = simple<o:p></o:p></p><p class=MsoNormal>nstlist = 0<o:p></o:p></p><p class=MsoNormal>rlist = 0<o:p></o:p></p><p class=MsoNormal>coulombtype = cut-off<o:p></o:p></p><p class=MsoNormal>rcoulomb = 0<o:p></o:p></p><p class=MsoNormal>vdwtype = cut-off<o:p></o:p></p><p class=MsoNormal>rvdw = 0<o:p></o:p></p><p class=MsoNormal>nstcalcenergy = 1<o:p></o:p></p><p class=MsoNormal>nstenergy = 1<o:p></o:p></p><p class=MsoNormal>emtol = 0<o:p></o:p></p><p class=MsoNormal>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The only changes from the former .mdp file are in nsteps and nstenergy.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>However, when I run this potential energy status run on em3.gro itself,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>grompp -f status.mdp -p topol.top -c em3.gro -o status.tpr -po status.mdout.mdp<o:p></o:p></p><p class=MsoNormal>mdrun -nice 0 -v -pd -deffnm status<o:p></o:p></p><p class=MsoNormal>g_energy -s status.tpr -f status.edr -o status.potential_energy.xvg<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>and look at the (single) energy line in status.potential_energy.xvg I find that the energy does not agree with the one obtained during minimization (it’s higher by some tens of kJ/mol).<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>What am I doing wrong? How should one reliably find the energy of a given .gro file?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Moreover, when changing in status.mdp to integrator = steep, the results also change dramatically – why should the algorithm matter if no steps are performed and the initial structure is explored?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thanks,<o:p></o:p></p><p class=MsoNormal>Ehud.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>