Re: [Apbs-users] convergent problem related to the grid size

[Gernot K. <ge...@ch...>]

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