Thread: Re: [Apbs-users] SDH in APBS 0.5.0
Biomolecular electrostatics software
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From: Bradley S. P. <bs...@ge...> - 2007-05-25 22:33:51
Attachments:
4fsr_ar.pqr
1hip_ar.pqr
|
Nathan, Thank you for the reply. Attached are the pqr files. -Scott ----- Original Message ----- From: Nathan Baker <ba...@cc...> Date: Friday, May 25, 2007 6:16 pm Subject: Re: [Apbs-users] SDH in APBS 0.5.0 > Hello -- > > That's strange. Based on the changes made (added multipole > support) > for 'bcfl sdh' in version 0.5.0, it should behave *less* like 'bcfl > > zero'. Can you send the PQR file so we can test this? > > Thanks, > > Nathan > > On May 25, 2007, at 2:20 PM, Bradley Scott Perrin wrote: > > > Hello APBS Users, > > > > In APBS 0.5.0, I received the same result using 'bcfl sdh' as > 'bcfl > > zero'. When performing the same calculation under APBS 0.4.0, > 'bcfl > > sdh' gave much better numbers than 'bcfl zero' (as expected). > > > > Any ideas on how I managed this? > > > > I've attached a sample input file. The size of the molecule is > > roughly 45 x 45 x 45 A^3. > > > > -Scott > > <test_sdh.in> > > ------------------------------------------------------------------ > ---- > > --- > > 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: Bradley S. P. <bs...@ge...> - 2007-05-27 14:47:31
|
Thank you for your help. I'll try 'bcfl mdh'. -Scott ----- Original Message ----- From: Nathan Baker <ba...@cc...> Date: Saturday, May 26, 2007 8:59 pm Subject: Re: [Apbs-users] SDH in APBS 0.5.0 > Hello -- > > Yes, you're correct: 'bcfl sdh' appears to be behaving like 'bcfl > > zero'. New boundary condition code was added into APBS in version > > 0.5.0. This code doesn't affect 'bcfl mdh' or focusing. > > We'll take a look at this and see if we can fix it quickly. In > the > meantime, I'd suggest using 'bcfl mdh'. > > Sorry for any inconvenience this might cause. > > -- Nathan > > > On May 25, 2007, at 5:32 PM, Bradley Scott Perrin wrote: > > > Nathan, > > > > Thank you for the reply. Attached are the pqr files. > > > > -Scott > > > > > > ----- Original Message ----- > > From: Nathan Baker <ba...@cc...> > > Date: Friday, May 25, 2007 6:16 pm > > Subject: Re: [Apbs-users] SDH in APBS 0.5.0 > > > >> Hello -- > >> > >> That's strange. Based on the changes made (added multipole > >> support) > >> for 'bcfl sdh' in version 0.5.0, it should behave *less* like 'bcfl > >> > >> zero'. Can you send the PQR file so we can test this? > >> > >> Thanks, > >> > >> Nathan > >> > >> On May 25, 2007, at 2:20 PM, Bradley Scott Perrin wrote: > >> > >>> Hello APBS Users, > >>> > >>> In APBS 0.5.0, I received the same result using 'bcfl sdh' as > >> 'bcfl > >>> zero'. When performing the same calculation under APBS 0.4.0, > >> 'bcfl > >>> sdh' gave much better numbers than 'bcfl zero' (as expected). > >>> > >>> Any ideas on how I managed this? > >>> > >>> I've attached a sample input file. The size of the molecule is > >>> roughly 45 x 45 x 45 A^3. > >>> > >>> -Scott > >>> <test_sdh.in> > >>> --------------------------------------------------------------- > --- > >> ---- > >>> --- > >>> 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/ > >> > >> > >> <4fsr_ar.pqr> > >> <1hip_ar.pqr> > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > |
From: Nathan B. <ba...@cc...> - 2007-05-27 14:56:17
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Hi All -- We've checked in a version (revision 1094) of APBS into Subversion which fixes this issue. Our Subversion repository is publicly- accessible using the instructions at http://sourceforge.net/svn/?group_id=148472 We'll hurry to prepare an official release of APBS which incorporates this bug fix. Thanks Scott for finding this! -- Nathan On May 27, 2007, at 9:47 AM, Bradley Scott Perrin wrote: > Thank you for your help. I'll try 'bcfl mdh'. > > -Scott > > ----- Original Message ----- > From: Nathan Baker <ba...@cc...> > Date: Saturday, May 26, 2007 8:59 pm > Subject: Re: [Apbs-users] SDH in APBS 0.5.0 > >> Hello -- >> >> Yes, you're correct: 'bcfl sdh' appears to be behaving like 'bcfl >> >> zero'. New boundary condition code was added into APBS in version >> >> 0.5.0. This code doesn't affect 'bcfl mdh' or focusing. >> >> We'll take a look at this and see if we can fix it quickly. In >> the >> meantime, I'd suggest using 'bcfl mdh'. >> >> Sorry for any inconvenience this might cause. >> >> -- Nathan >> >> >> On May 25, 2007, at 5:32 PM, Bradley Scott Perrin wrote: >> >>> Nathan, >>> >>> Thank you for the reply. Attached are the pqr files. >>> >>> -Scott >>> >>> >>> ----- Original Message ----- >>> From: Nathan Baker <ba...@cc...> >>> Date: Friday, May 25, 2007 6:16 pm >>> Subject: Re: [Apbs-users] SDH in APBS 0.5.0 >>> >>>> Hello -- >>>> >>>> That's strange. Based on the changes made (added multipole >>>> support) >>>> for 'bcfl sdh' in version 0.5.0, it should behave *less* like 'bcfl >>>> >>>> zero'. Can you send the PQR file so we can test this? >>>> >>>> Thanks, >>>> >>>> Nathan >>>> >>>> On May 25, 2007, at 2:20 PM, Bradley Scott Perrin wrote: >>>> >>>>> Hello APBS Users, >>>>> >>>>> In APBS 0.5.0, I received the same result using 'bcfl sdh' as >>>> 'bcfl >>>>> zero'. When performing the same calculation under APBS 0.4.0, >>>> 'bcfl >>>>> sdh' gave much better numbers than 'bcfl zero' (as expected). >>>>> >>>>> Any ideas on how I managed this? >>>>> >>>>> I've attached a sample input file. The size of the molecule is >>>>> roughly 45 x 45 x 45 A^3. >>>>> >>>>> -Scott >>>>> <test_sdh.in> >>>>> --------------------------------------------------------------- >> --- >>>> ---- >>>>> --- >>>>> 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/ >>>> >>>> >>>> <4fsr_ar.pqr> >>>> <1hip_ar.pqr> >> >> -- >> Associate Professor, Dept. of Biochemistry and Molecular Biophysics >> Center for Computational Biology, Washington University in St. Louis >> Web: http://cholla.wustl.edu/ >> >> -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Nathan B. <ba...@cc...> - 2007-05-27 01:00:00
|
Hello -- Yes, you're correct: 'bcfl sdh' appears to be behaving like 'bcfl zero'. New boundary condition code was added into APBS in version 0.5.0. This code doesn't affect 'bcfl mdh' or focusing. We'll take a look at this and see if we can fix it quickly. In the meantime, I'd suggest using 'bcfl mdh'. Sorry for any inconvenience this might cause. -- Nathan On May 25, 2007, at 5:32 PM, Bradley Scott Perrin wrote: > Nathan, > > Thank you for the reply. Attached are the pqr files. > > -Scott > > > ----- Original Message ----- > From: Nathan Baker <ba...@cc...> > Date: Friday, May 25, 2007 6:16 pm > Subject: Re: [Apbs-users] SDH in APBS 0.5.0 > >> Hello -- >> >> That's strange. Based on the changes made (added multipole >> support) >> for 'bcfl sdh' in version 0.5.0, it should behave *less* like 'bcfl >> >> zero'. Can you send the PQR file so we can test this? >> >> Thanks, >> >> Nathan >> >> On May 25, 2007, at 2:20 PM, Bradley Scott Perrin wrote: >> >>> Hello APBS Users, >>> >>> In APBS 0.5.0, I received the same result using 'bcfl sdh' as >> 'bcfl >>> zero'. When performing the same calculation under APBS 0.4.0, >> 'bcfl >>> sdh' gave much better numbers than 'bcfl zero' (as expected). >>> >>> Any ideas on how I managed this? >>> >>> I've attached a sample input file. The size of the molecule is >>> roughly 45 x 45 x 45 A^3. >>> >>> -Scott >>> <test_sdh.in> >>> ------------------------------------------------------------------ >> ---- >>> --- >>> 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/ >> >> >> <4fsr_ar.pqr> >> <1hip_ar.pqr> -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |