Thread: [Apbs-users] calcenergy for npbe
Biomolecular electrostatics software
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From: Andrew <af...@vt...> - 2008-12-22 21:07:56
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Hi all, I was looking around the web and the posted tutorials to try and find a definitive answer as to whether or not the energy reported from calcenergy for the nonlinear solver includes the osmotic pressure and electrostatic stress terms as shown in Sharp and Honig (1990), but I was unable to find the answer so I figured I'll ask you guys. Also, when running the nonlinear solver on large structures with large grids (481x481x481+), are there any pitfalls I need to look out for that do not appear for small systems? Thanks for your help! Cheers, Andrew |
From: Nathan B. <ba...@bi...> - 2008-12-23 20:04:07
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Hi Andrew -- I was looking around the web and the posted tutorials to try and find > a definitive answer as to whether or not the energy reported from > calcenergy for the nonlinear solver includes the osmotic pressure and > electrostatic stress terms as shown in Sharp and Honig (1990), but I > was unable to find the answer so I figured I'll ask you guys. Yes, it does include that term. > Also, when running the nonlinear solver on large structures with > large grids (481x481x481+), are there any pitfalls I need to look out > for that do not appear for small systems? Not that I'm aware of. Thanks, Nathan > > Thanks for your help! > > Cheers, > Andrew > > > ------------------------------------------------------------------------------ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |