GROMACS

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)

Settings

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.

Modules

Energies

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

Timing

Data sources:

• <module cmlx:templateRef='hardware'>

• <module cmlx:templateRef='summary'>

• <module cmlx:templateRef='accounting'>

[^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>