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

[Mark Abraham]

I would look at the PME initialization code to do the intercept. Or if a
rerun would suffice, combine the terms from runs on topologies with
different charge on Cl
On Aug 7, 2013 3:29 AM, "Shi, Yu (shiy4)" <shiy4 at mail.uc.edu> wrote:

> 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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