README for alkane nonpolar solvation APBS example

$Id: README.html 916 2006-07-29 20:44:09Z sobolevnrm $

The example input files in this directory calculate nonpolar solvation energies for alkanes based on the protocol described in Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006. (http://dx.doi.org/10.1073/pnas.0600118103).

This example was contributed by Nathan Baker and Jason Wagoner.

Output files are generated and executed by the runme.sh script.

APBS Version Alkane SASA (Å2) SASA energy (kJ/mol) SAV (Å3) SAV energy (kJ/mol) WCA energy (kJ/mol) Total nonpolar solvation energy (kJ/mol)
0.5.1 2-methylbutane 214.202 1.82072 253.906 60.7852 -48.3035 1.439739455792E+01
butane 193.855 1.64777 218.119 52.2176 -41.6443 1.208346456826E+01
cyclohexane 221.799 1.88529 267.165 63.9593 -52.4787 1.354016672221E+01
cyclopentane 193.638 1.64593 218.412 52.2877 -44.3607 9.363673200142E+00
ethane 139.427 1.18513 140.692 33.6818 -25.4382 9.422717598546E+00
hexane 250.291 2.12748 297.703 71.2701 -57.1544 1.640068943201E+01
isobutane 192.744 1.63832 219.153 52.4652 -40.8617 1.323144287435E+01
methane 105.42 0.896066 95.4242 22.8446 -15.9414 7.894367190329E+00
neopentane 210.755 1.79141 251.314 60.1647 -47.4807 1.449633815052E+01
pentane 222.524 259.149 1.89145 62.0403 -49.456 1.447900211546E+01
propane 170.391 182.703 1.44832 43.739 -33.4629 1.192358496286E+01

APBS Version Alkane SASA (Å2) SASA energy (kJ/mol) SAV (Å3) SAV energy (kJ/mol) WCA energy (kJ/mol) Total nonpolar solvation energy (kJ/mol)
0.5.0 2-methylbutane 214.202 1.82072 253.906 60.7852 -48.3035 1.430239579640E+01
butane 193.855 1.64777 218.119 52.2176 -41.6443 1.222110127537E+01
cyclohexane 221.799 1.88529 267.165 63.9593 -52.4787 1.336586748209E+01
cyclopentane 193.638 1.64593 218.412 52.2877 -44.3607 9.572911268235E+00
ethane 139.427 1.18513 140.692 33.6818 -25.4382 9.428701470984E+00
hexane 250.291 2.12748 297.703 71.2701 -57.1544 1.624316652259E+01
isobutane 192.744 1.63832 219.153 52.4652 -40.8617 1.324178842307E+01
methane 105.42 0.896066 95.4242 22.8446 -15.9414 7.799212389992E+00
neopentane 210.755 1.79141 251.314 60.1647 -47.4807 1.447540747648E+01
pentane 222.524 259.149 1.89145 62.0403 -49.456 1.447574303821E+01
propane 170.391 182.703 1.44832 43.739 -33.4629 1.172438897305E+01

1 The discrepancy in values between versions 0.5.1 and 0.5.0 is most likely due to the following factor(s):

Please see the ChangeLog or the APBS documentation for more information.