apbs-users

 [Apbs-users] : elec force focusing From: matteo.rotter - 2009-12-21 15:21:49 ```Dear all, We are using apbs/1.2.1) for calculate the elec and apolar forces acting on a molecule in solvent through the Poisson Boltzmann equation. We use the mg-manual option to calulate first the results for a coarse grid and then the results for a fine grid, smaller than the coarse one. Center of the fine grid is different form the center of the coarse grid. What we find is that the fine grid didn't work due to the error: Vpmg_dbForce: Atom 7 off grid! VASSERT: ASSERTION FAILURE! filename routines.c, line 1205, (Vpmg_dbForce(pmg, (*atomForce)[j].dbForce, j, pbeparm->srfm)) Increasing glen little for the fine grid would bring to an error for another atom, (now atom 7 is in the grid) but in my mind that wasn't a good way to solve the problem.. Looking in the apbs-1.2.1-source/src/mg/vpmg.c we suppose that the problem is that the atom involved is in the grid, but his radius for calculation goes out of it. So we tried to find a way to solve the problem: Vpmg_dbForce: line 5542: original: /* Make sure we're on the grid */ if ((apos[0]<=xmin) || (apos[0]>=xmax) || \ (apos[1]<=ymin) || (apos[1]>=ymax) || \ (apos[2]<=zmin) || (apos[2]>=zmax)) { seems that would be better to calculate position < (xmin + rtot) and > (xmax - rtot) to include also the dimensions of splineWin in the calculation. /* Make sure we're on the grid */ if ((apos[0]<=xmin + rtot) || (apos[0]>=xmax - rtot) || \ (apos[1]<=ymin + rtot) || (apos[1]>=ymax - rtot) || \ (apos[2]<=zmin + rtot) || (apos[2]>=zmax - rtot)) { Would also be better to include the radius of solvent in the calculation of rtot: rtot = (arad + thee->splineWin + srad); Now the calulation works without errors. What do you think about our changes? Regards, Matteo. ```
 Re: [Apbs-users] : elec force focusing From: Nathan Baker - 2009-12-21 16:56:48 Attachments: Message as HTML ```Hello -- This looks like a good addition to the grid checking. Yong/Dave, can you test this out and see if it works with other features in the code? Thank you very much for your fix and help with APBS! -- Nathan On Mon, Dec 21, 2009 at 8:58 AM, matteo.rotter wrote: > Dear all, > > We are using apbs/1.2.1) for calculate the elec and apolar forces > acting on a molecule in solvent through the Poisson Boltzmann equation. > We use the mg-manual option to calulate first the results for a coarse > grid and then the results for a fine grid, smaller than the coarse one. > Center of the fine grid is different form the center of the coarse grid. > > What we find is that the fine grid didn't work due to the error: > Vpmg_dbForce: Atom 7 off grid! > VASSERT: ASSERTION FAILURE! filename routines.c, line 1205, > (Vpmg_dbForce(pmg, (*atomForce)[j].dbForce, j, pbeparm->srfm)) > Increasing glen little for the fine grid would bring to an error for > another atom, (now atom 7 is in the grid) but in my mind that wasn't a > good way to solve the problem.. > Looking in the apbs-1.2.1-source/src/mg/vpmg.c we suppose that the > problem is that the atom involved is in the grid, but his radius for > calculation goes out of it. > So we tried to find a way to solve the problem: > > Vpmg_dbForce: > line 5542: original: > /* Make sure we're on the grid */ > if ((apos[0]<=xmin) || (apos[0]>=xmax) || \ > (apos[1]<=ymin) || (apos[1]>=ymax) || \ > (apos[2]<=zmin) || (apos[2]>=zmax)) { > > > seems that would be better to calculate position < (xmin + rtot) and > > (xmax - rtot) to include also the dimensions of splineWin in the > calculation. > > /* Make sure we're on the grid */ > if ((apos[0]<=xmin + rtot) || (apos[0]>=xmax - rtot) || \ > (apos[1]<=ymin + rtot) || (apos[1]>=ymax - rtot) || \ > (apos[2]<=zmin + rtot) || (apos[2]>=zmax - rtot)) { > > > > Would also be better to include the radius of solvent in the calculation > of rtot: > rtot = (arad + thee->splineWin + srad); > > Now the calulation works without errors. > What do you think about our changes? > > Regards, > > Matteo. > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and > easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > apbs-users mailing list > apbs-users@... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- Nathan Baker (http://bakergroup.wustl.edu) Associate Professor, Dept. of Biochemistry and Molecular Biophysics Director, Computational and Molecular Biophysics Graduate Program Center for Computational Biology, Washington University in St. Louis ```