[gmx-users] set charge as 0 in gromacs code

[Mark Abraham]

Ewald self energy, perhaps?

Mark

On Wed, Aug 7, 2013 at 1:16 AM, Shi, Yu (shiy4) <shiy4 at 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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