Thread: [Apbs-users] convergent problem related to the grid size
Biomolecular electrostatics software
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From: Haiguang L. <hai...@gm...> - 2008-06-30 21:12:14
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Hi everyone, I am doing APBS calculations on a protein system with two conformations. I would like to get the electrostatic energy difference between the two conformations. However, when I fixed the box size and changed the grid size (by changing the number of grid points along each axis), the energy differences seem to be too big. I set the center of the grid to be the center of the molecule in both conformations. I used exactly the same input parameters except changing dime. The energy I obtained got bigger when the grid is getting finer. Can anyone tell me the possible reason? or is there any mistakes in my input file? Here is the input parameters: ///////////////////////////////////// read mol pqr ack_last.pqr end elec name first mg-auto dime 353 481 289 cglen 186.0 213.0 134.0 cgcent mol 1 fglen 146 173 95 fgcent mol 1 mol 1 lpbe bcfl sdh srfm smol chgm spl2 ion 1 0.150 0.95 ion -1 0.150 1.81 pdie 2.0 sdie 78.54 sdens 10.0 srad 1.4 swin 0.3 temp 298.15 gamma 0.105 calcenergy total calcforce no write pot dx pot end print energy first end quit //////////////////////////// Thanks, Cheers, Haiguang |
From: Gernot K. <ge...@ch...> - 2008-07-02 08:07:26
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Hi! Haiguang Liu schrieb: > Hi everyone, > I am doing APBS calculations on a protein system with two > conformations. I would like to get the electrostatic energy difference > between the two conformations. However, when I fixed the box size and > changed the grid size (by changing the number of grid points along each > axis), the energy differences seem to be too big. If you change the number of grid points and keep the box dimension constant, you will change the grid resolution. If the resolution is different in both cases, the grid artefact won't cancel. > ///////////////////////////////////// > read > mol pqr ack_last.pqr > end > elec name first > mg-auto > dime 353 481 289 > cglen 186.0 213.0 134.0 > cgcent mol 1 > fglen 146 173 95 BTW: your focusing protocol is suboptimal. I would start with a much larger coarse grid (resolution ~ 1-3 Angstroms). A max. resolution of 0.5 Angstr might be enough, so could use less grid points just to speed things up. Best regards, Gernot Kieseritzky |