Amber

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

General Info

Amber - 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	header template	Amber 18
Author	Username fullname	Doe, John
Calculation type	Custom logic 1	Molecular Dynamics (NPT)

Settings

This section captures initialization settings like starting time, timestep used, pressure and temperature regulation, etc.

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

Atomic coordinates

After settings, our HTML resume will output a coordinates table with current molecule atoms and its cell dimensions.

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

Information its read from parameter/topology file specification and trajectory restart file. Solvent atoms will be discarded.

Modules

Averages

Data sources:

• <module cmlx:templateRef=’averages’>

• <module cmlx:templateRef=’results’>

Timing

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

1

string amber:getMethod string imin string ntt string ntp

    $imin  Variable imin from module <module cmlx:templateRef="control" >
    $ntt  Variable ntt from module <module cmlx:templateRef="control" >
    $ntp  Variable ntp from module <module cmlx:templateRef="control" >

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

    <xsl:param name="imin" />
    <xsl:param name="ntp" />
    <xsl:param name="ntt" />

    <xsl:choose>
        <xsl:when test="exists($imin) and number($imin) = 1">
            <xsl:value-of select="$am:GeometryOptimization" />
        </xsl:when>
        <xsl:when test="exists($ntp) and number($ntp) &gt; 0">
            <xsl:value-of select="$am:npt"/>
        </xsl:when>
        <xsl:otherwise>
            <xsl:choose>
                <xsl:when test="exists($ntt) and number($ntt) = 0">
                    <xsl:value-of select="$am:nve"/>
                </xsl:when>
                <xsl:otherwise>
                    <xsl:value-of select="$am:nvt"/>
                </xsl:otherwise>
            </xsl:choose>
        </xsl:otherwise>
    </xsl:choose>