Ewald self energy, perhaps?
Mark
On Wed, Aug 7, 2013 at 1:16 AM, Shi, Yu (shiy4) <sh...@mail.uc.edu> wrote:
> Hello everyone,
>
> My system is 512 waters and 1 ion CL-. Now I would like to change the CL
> charge as 0 in the gromacs code for the short non-bonded interaction. While
> for the long-range electrostatics (pme) the CL is -1.
>
> My gromacs version is 4.6.2, which automatically starts 8 threads to
> compute.
>
> In src/kernel/md.c, at line 1191 just before function do_force() , I added
> codes as following which could find out which atom is CL and change its
> charge as 0 in a certain thread. After this, when I use g_energy, the
> Coul.SR of SOL and CL is -88 kJ, which should be 0 kJ.
>
> Does anyone could help me out?
>
> int stone_a;
> for (stone_a=mdatoms->start;
> stone_a<mdatoms->start+mdatoms->homenr; stone_a++)
> {
> if (mdatoms->chargeA[stone_a] == -1.0)
> {
> fprintf(stderr,"the atom %d found with charge %f\n",
> stone_a,mdatoms->chargeA[stone_a]);
> mdatoms->chargeA[stone_a]=0.0;
> break;
> }
> }
>
> Thanks,
>
> Stony
>
> --
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