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steep ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceGROMACS log
idsteep
nameSteepest Descents
pattern\s*Initiating\sSteepest\sDescents.*
endPattern\s*Finished\smdrun\son\srank.*
endPattern2~
endOffset1
xml:basejob/steep.xml

Input ​

Initiating Steepest Descents
Started Steepest Descents on rank 0 Thu Mar 24 08:07:52 2022


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
           Step           Time
              0        0.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    3.49730e+05   -8.70966e+05    1.28223e+04   -5.08413e+05    2.95889e+04

           Step           Time
              1        1.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    2.97313e+05   -8.71936e+05    1.27724e+04   -5.61851e+05    2.20612e+04

           Step           Time
              2        2.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    2.48541e+05   -8.73970e+05    1.26300e+04   -6.12799e+05    1.51424e+04

           Step           Time
              3        3.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    2.11290e+05   -8.77578e+05    1.23070e+04   -6.53981e+05    9.59498e+03

           Step           Time
              4        4.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    1.86020e+05   -8.83698e+05    1.16364e+04   -6.86042e+05    5.63078e+03

           Step           Time
              5        5.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    1.64635e+05   -8.95427e+05    1.01248e+04   -7.20668e+05    1.99876e+03

           Step           Time
              6        6.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    1.54818e+05   -9.06953e+05    8.62540e+03   -7.43510e+05    5.09000e+01

           Step           Time
              7        7.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    1.51869e+05   -9.10532e+05    8.23930e+03   -7.50424e+05   -5.42049e+02

           Step           Time
              8        8.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    1.43465e+05   -9.25094e+05    6.61912e+03   -7.75010e+05   -2.40643e+03

           Step           Time
              9        9.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    1.41340e+05   -9.28615e+05    6.39286e+03   -7.80882e+05   -2.87211e+03


step 10: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
           Step           Time
             10       10.00000

           Step           Time
             11       11.00000

   Energies (kJ/mol)
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential Pressure (bar)
    1.38180e+05   -9.35808e+05    5.83706e+03   -7.91790e+05   -3.64690e+03


Steepest Descents converged to Fmax < 1000 in 12 steps
Potential Energy  = -7.9178994e+05
Maximum force     =  7.6484247e+02 on atom 91
Norm of force     =  1.2360245e+02
Finished mdrun on rank 0 Thu Mar 24 08:07:53 2022

Current template has input comments defined but it's output is missing, please notify software developers.

Template definition ​

xml
<record repeat="1" />
<record>\s*Started\sSteepest\sDescents\son\srank\s+\S+\s+&#123;X,cc:runDate&#125;</record>
<templateList>  <template id="energies" pattern="\s*Energies\s+\(kJ\/mol\).*" endPattern=".*[0-9]\s*$\s*" endOffset="1" repeat="*">    <record repeat="1" />    <record>&#123;A15,x:label&#125;&#123;A15,x:label&#125;&#123;A15,x:label&#125;&#123;A15,x:label&#125;&#123;A15,x:label&#125;</record>    <record>&#123;E,x:value&#125;&#123;E,x:value&#125;&#123;E,x:value&#125;&#123;E,x:value&#125;&#123;E,x:value&#125;</record>                            
        </template>  <template id="endDate" pattern="\s*Finished\smdrun\son.*" endPattern=".*" endPattern2="~">    <record>\s*Finished\smdrun\son\srank\s+\S+\s+&#123;X,cc:jobdatetime.end&#125;</record>
        </template>   
    </templateList>
<transform process="delete" xpath=".//cml:module[@cmlx:templateRef='energies'][position() != last()]" />
<transform process="createWrapper" xpath=".//cml:scalar[@dictRef='x:label']" elementName="cml:property" />
<transform process="pullup" xpath=".//cml:property" repeat="2" />
<transform process="pullup" xpath=".//cml:scalar[@dictRef='x:value']" repeat="2" />
<transform process="moveRelative" xpath="./cml:module[@cmlx:templateRef='energies']/cml:scalar[@dictRef='x:value']" to="./preceding-sibling::cml:property[not(exists(cml:scalar[@dictRef='x:value']))][position() =1]" />
<transform process="createDate" xpath=".//cml:scalar[@dictRef='cc:runDate']" format="E MMM  d HH:mm:ss yyyy" />
<transform process="createDate" xpath=".//cml:scalar[@dictRef='cc:runDate']" format="E MMM dd HH:mm:ss yyyy" />
<transform process="createDate" xpath=".//cml:scalar[@dictRef='cc:jobdatetime.end']" format="E MMM  d HH:mm:ss yyyy" />
<transform process="createDate" xpath=".//cml:scalar[@dictRef='cc:jobdatetime.end']" format="E MMM dd HH:mm:ss yyyy" />
<transform process="pullup" xpath=".//cml:scalar[@dictRef='cc:runDate']" />
<transform process="pullup" xpath=".//cml:scalar[@dictRef='cc:jobdatetime.end']" repeat="2" />
<transform process="delete" xpath=".//cml:list" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />