GROMACS

For this specific format, the most relevant information is the trajectory file in its binary form (.xtc), mandatory on all uploads. ioChem-BD won’t render such files but keep them inside the platform for its later download.

General Info

GROMACS - General Info - Main fields
Field Source Sample value
Title Set on Browse calculation publication Sample calculation
Browse Item URL pointing Browse published item https://iochem-bd.iciq.es/browse/handle/100/5672
Program program.header template GROMACS 5.0.2
Author Username fullname Doe, John
Calculation type Fixed value (method used) [1] Molecular Dynamics (NPT)
../_images/GROMACS_header.png

Settings

This section captures initialization settings like starting time, timestep used, coupling groups, etc.

Data source: <module cmlx:templateRef=’input.parameters’>

../_images/GROMACS_settings.png

Atomic coordinates

After settings, our HTML resume will output a xyz coordinates table with current molecule atoms.

For every atom, we will output it’s serial number, atom type, coordinates in angstroms.

Information its read from molecular structure file.

../_images/GROMACS_geometry.png

Modules

Energies

Data source: <module cmlx:templateRef=’averages’>

../_images/GROMACS_module_energies.png

Timing

Data sources:

  • <module cmlx:templateRef=’hardware’>
  • <module cmlx:templateRef=’summary’>
  • <module cmlx:templateRef=’accounting’>
../_images/GROMACS_module_timing.png
[1]

string gromacs:getCalcType string tcoupl string pcoupl

$tcoupl  Variable tcoupl from module <module cmlx:templateRef="input" >
$pcoupl  Variable pcoupl from module <module cmlx:templateRef="input" >

<!-- Calculation type related constants -->
<xsl:variable name="gm:npt">NPT</xsl:variable>
<xsl:variable name="gm:nvt">NVT</xsl:variable>
<xsl:variable name="gm:nve">NVE</xsl:variable>

<xsl:param name="tcoupl"  />
<xsl:param name="pcoupl" />

<xsl:choose>
    <xsl:when test="not(exists($pcoupl)) or lower-case(gm:trim($pcoupl/text())) = 'no'">
        <xsl:choose>
            <xsl:when test="not(exists($tcoupl)) or lower-case(gm:trim($tcoupl/text())) = 'no'">
                <xsl:value-of select="$gm:nve"/>
            </xsl:when>
            <xsl:otherwise>
                <xsl:value-of select="$gm:nvt"/>
            </xsl:otherwise>
        </xsl:choose>
    </xsl:when>
    <xsl:otherwise>
        <xsl:value-of select="$gm:npt"/>
    </xsl:otherwise>
</xsl:choose>