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

Shi, Yu (shiy4) shiy4 at mail.uc.edu
Wed Aug 7 01:16:32 CEST 2013

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]);



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