Negative surface area?

From: David Minh (daveminh_at_gmail.com)
Date: Fri Jun 15 2012 - 09:08:12 CDT

Hi NAMD users,

Has anyone else seen a negative surface area value?

I'm using NAMD 2.9 and get a negative surface area for a host-guest system.
 I see it for the host, and for the host-guest complex, but not for the
guest itself. An example is attached. Is this a quirk of the SASA
algorithm or is it a bug?

Thanks,
David

ETITLE: TS BOND ANGLE DIHED IMPRP
              ELECT VDW BOUNDARY MISC
 KINETIC TOTAL TEMP POTENTIAL TOTAL3
     TEMPAVG

Vacuum ENERGY: 0 0.8593 149.6652 34.6591
 23.1692 76.6095 -65.2340 0.0000 0.0000
     93.0849 312.8133 278.8241 219.7284
312.8224 278.8241

GB ENERGY: 0 0.8593 149.6652 34.6591
 23.1692 -70.1686 -65.2340 0.0000 0.0000
     93.0849 166.0352 278.8241 72.9503
166.0377 278.8241

GBSA ENERGY: 0 0.8593 149.6652 34.6591
 23.1692 -77.1064 -65.2340 0.0000 0.0000
     93.0849 159.0973 278.8241 66.0124
159.0998 278.8241

Info: NAMD 2.9 for Linux-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60400 for multicore-linux64-iccstatic
Info: Built Mon Apr 30 14:00:48 CDT 2012 by jim on naiad.ks.uiuc.edu
Info: 1 NAMD 2.9 Linux-x86_64-multicore 8 dnb09.chem.duke.edu dm225
Info: Running on 8 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00875401 s
Info: 549.258 MB of memory in use based on /proc/self/stat
Info: Configuration file is CUC_energy_vac.namd
Info: Working in the current directory
/xtmp/dm225/clusters/DSCR/Cu[7]/1-build/M
M2Examples/NAMD_Test


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