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

[Shi, Yu (shiy4)]

Hello Mark,

Thanks for your reply!!!

Not self energy term.

For my research reason, I would like to turn off the long-ranged electrostatics between 
SOL and CL. That is to say, SOL and CL only interacts with erfc(eta*r)/r potential, without
reciprocal electrostatics parts.

I use PME in the mdp file for coulomb, and in topol file the CL is -1 charged.
Hence I have to set CL charge as 0 in the Gromacs code to turn off the reciprocal calculation of
the pme scheme. E.g before gmx_pme_do(), I set Cl charge as 0, but this fails to work.

So do you some idea to do this?

Stony

________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [mark.j.abraham at gmail.com]
Sent: Tuesday, August 06, 2013 8:20 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] set charge as 0 in gromacs code

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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