Thread: [Apbs-users] calculating dipole moment
Biomolecular electrostatics software
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From: Ibrahim M. M. <I.m...@ps...> - 2007-06-01 20:50:09
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Dear users, I want to calculate the dipole moment of few proteins to compare and want to be able to visualize it; something similar to what GRASP does. I'm wondering if I can do that in APSB?!. thanks, Ibrahim ---------------------------------------------------------------------------------------------------------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 ---------------------------------------------------------------------------------------------------------- |
From: magdalena g. <mag...@wp...> - 2007-06-04 11:55:52
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dear All, does anyone know, whether it is possible to set up mg-para calculations on the grid with equal resolution in each direction? it seems to me, that APBS itself creates the grid, and the final resolution in each direction dependes on the initial parameters. can i force APBS to use "my" definition of final grid? or maybe there is a tool that maps values from one grid onto the other with specified grid resolution? i would be very grateful for help, best wishes, magdalena ---------------------------------------------------- Joe Cocker w Poznaniu! 24.06.2007 w poznańskiej Arenie zagra "Hymn for my soul" oraz najbardziej znane przeboje; organizator wwW.8gate.pl; bilety wwW.ticketpro.pl http://klik.wp.pl/?adr=http%3A%2F%2Fadv.reklama.wp.pl%2Fas%2Fcocker.html&sid=1177 |
From: Nathan B. <sob...@gm...> - 2007-06-05 22:37:16
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Hello -- > does anyone know, whether it is possible > to set up mg-para calculations on the grid > with equal resolution in each direction? This should be feasible by using an equal number of processors in =20 each direction. What has your experience been with this? > it seems to me, that APBS itself creates the grid, > and the final resolution in each direction dependes > on the initial parameters. > can i force APBS to use "my" definition of final grid? That's difficult since APBS is trying to ensure a certain degree of =20 overlap between the grid partitions. If you really want to do this =20 yourself, you could use a series of mg-manual calculations. > or maybe there is a tool that maps values from one grid > onto the other with specified grid resolution? Yes, please see apbs/tools/mesh/mergedx2. Thanks, Nathan > i would be very grateful for help, > best wishes, > magdalena > > ---------------------------------------------------- > Joe Cocker w Poznaniu! 24.06.2007 w pozna=C5=84skiej Arenie > zagra "Hymn for my soul" oraz najbardziej znane przeboje; > organizator wwW.8gate.pl; bilety wwW.ticketpro.pl > http://klik.wp.pl/?adr=3Dhttp%3A%2F%2Fadv.reklama.wp.pl%2Fas%=20 > 2Fcocker.html&sid=3D1177 > > > > ----------------------------------------------------------------------=20= > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > 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/ |
From: Magdalena G. <M.G...@ic...> - 2007-06-06 08:51:12
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hi Nathan, thanks for reply. > > This should be feasible by using an equal number of processors in > each direction. What has your experience been with this? > the number of processors depends significantly on our cluster possibilities. i tried calculations on 4x2x2 processors. the resulting resolution was 0.625 x 0.658 x 0.633. so it is almost equal in each direction, but "almost" is not enough. however, even in the directions where the number of processors was equal (y and z), the resolution is not equal. [i need to run uhbd, that's why i need equal grid spacing. and the system is huge. and unfortunately pdime 3x3x3 is not very suitable for our cluster] > Yes, please see apbs/tools/mesh/mergedx2. > do you mean mergedx or some other version mergedx2? i cannot find it in any latest APBS ditributions.. thanks magdalena |
From: magdalena g. <mag...@wp...> - 2007-06-06 09:27:27
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hi Nathan, thanks for reply. > This should be feasible by using an equal number of processors in > each direction. What has your experience been with this? the number of processors depends significantly on our cluster possibilities. i tried calculations on 4x2x2 processors. the resulting resolution was 0.625 x 0.658 x 0.633. so it is almost equal in each direction, but "almost" is not enough. however, even in the directions where the number of processors was equal (y and z), the resolution is not equal. [i need to run uhbd, that's why i need equal grid spacing. and the system is huge. and unfortunately pdime 3x3x3 is not very suitable for our cluster] > Yes, please see apbs/tools/mesh/mergedx2. do you mean mergedx or some other version mergedx2? i cannot find mergedx2 it in any latest APBS ditributions.. thanks magdalena ---------------------------------------------------- Po czym poznasz czy lato jest dobre? Po początku! A Lato zaczyna się w Gdyni! 23 czerwca http://klik.wp.pl/?adr=http%3A%2F%2Fadv.reklama.wp.pl%2Fas%2Fd112.html&sid=1178 |
From: Nathan B. <sob...@gm...> - 2007-06-06 12:22:11
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Hi Magdalena -- > the number of processors depends significantly on our cluster > possibilities. > i tried calculations on 4x2x2 processors. the resulting resolution was > 0.625 x 0.658 x 0.633. > so it is almost equal in each direction, but "almost" is not enough. > however, even in the directions where the number of processors > was equal (y and z), the resolution is not equal. > [i need to run uhbd, that's why i need equal grid spacing. > and the system is huge. and unfortunately pdime 3x3x3 > is not very suitable for our cluster] Please keep the "async" option in mind when running these calculations (see http://apbs.sourceforge.net/doc/user-guide/ index.html#elec-async for more information). This will allow you to run the processes of the parallel job asynchronously, thus eliminating any restrictions due to cluster size. >> Yes, please see apbs/tools/mesh/mergedx2. > > do you mean mergedx or some other version mergedx2? > i cannot find mergedx2 it in any latest APBS ditributions.. Oops! I forgot that this is in the developmental version of APBS (see http://sourceforge.net/svn/?group_id=148472 for download information). The existing mergedx has some of this functionality but mergedx2 is much easier to use and more reliable. Thanks, Nathan -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |