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
Program program.header template GROMACS 5.0.2
Author Username fullname Doe, John
Calculation type Fixed value (method used) [1] Molecular Dynamics (NPT)


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

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


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.




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



Data sources:

  • <module cmlx:templateRef=’hardware’>
  • <module cmlx:templateRef=’summary’>
  • <module cmlx:templateRef=’accounting’>

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