steep¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
| Attribute | Value |
|---|---|
| source | GROMACS log |
| id | steep |
| name | Steepest Descents |
| pattern | \s*Initiating\sSteepest\sDescents.* |
| endPattern | \s*Finished\smdrun\son\srank.* |
| endPattern2 | ~ |
| endOffset | 1 |
| xml:base | job/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
Warning
Current template has input comments defined but it’s output is missing, please notify software developers.
Template definition
<record repeat="1" />
<record>\s*Started\sSteepest\sDescents\son\srank\s+\S+\s+{X,cc:runDate}</record>
<templateList> <template id="energies" pattern="\s*Energies\s+\(kJ\/mol\).*" endPattern=".*[0-9]\s*$\s*" endOffset="1" repeat="*"> <record repeat="1" /> <record>{A15,x:label}{A15,x:label}{A15,x:label}{A15,x:label}{A15,x:label}</record> <record>{E,x:value}{E,x:value}{E,x:value}{E,x:value}{E,x:value}</record>
</template> <template id="endDate" pattern="\s*Finished\smdrun\son.*" endPattern=".*" endPattern2="~"> <record>\s*Finished\smdrun\son\srank\s+\S+\s+{X,cc:jobdatetime.end}</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]" />