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:
mol pqr ack_last.pqr
elec name first
dime 353 481 289
cglen 186.0 213.0 134.0
cgcent mol 1
fglen 146 173 95
fgcent mol 1
ion 1 0.150 0.95
ion -1 0.150 1.81
write pot dx pot
print energy first end
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.
> mol pqr ack_last.pqr
> elec name first
> 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
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