[gmx-developers] Wrong results when using Verlet cut-off scheme and ewald-geometry= 3DC in version 4.6 and higher

[Berk Hess]

Hi,

You are right. I filed a redmine issue:
http://redmine.gromacs.org/issues/1916
And I uploaded a fix for the release-5-0 branch:
https://gerrit.gromacs.org/#/c/5701/

Thanks for reporting this.

Cheers,

Berk

On 03/08/2016 04:11 AM, Sheng Bi wrote:
>
> Here we find gromacs goes wrong when using verlet and 3dc an run in 
> parallel.
>
> For slab geometry, we need to do slab correction based on total charge 
> dipole ( mu_tot=sum(qi*zi) ). If one performs such simulation in 
> gromacs with Verlet and 3dc in parallel (especially using domain 
> decomposition), the mu_tot is wrong. For example, if you run 
> simulation in 16 core, and the right global charge dipole is A, 
> however in gmx 4.6 and higher each core would get 16*A!
>
> I think the problem come out on this communication, for version 4.6, 
> gmx sum charge dipole twice. In sim_util.c, line 1052:
>
>             /* When we don't need the total dipole we sum it in 
> global_stat */
>
>             if (bStateChanged && NEED_MUTOT(*inputrec))
>
>             {
>
>                 gmx_sumd(2*DIM, mu, cr);
>
>             }
>
> if using domain decomposition, gmx will sum the dipole for the first 
> time. However in line 1090:
>
>      if (bStateChanged && NEED_MUTOT(*inputrec))
>
>     {
>
>         if (PAR(cr))
>
>         {
>
>             gmx_sumd(2*DIM, mu, cr);
>
>         }
>
>         for (i = 0; i < 2; i++)
>
>         {
>
>             for (j = 0; j < DIM; j++)
>
>             {
>
>                 fr->mu_tot[i][j] = mu[i*DIM + j];
>
>             }
>
>         }
>
>     }
>
> gmx sum the dipole for second time only if run in parallel. So, if you 
> perform simulation in 3dc with verlet and in domain decomposition, the 
> mu_tot will go wrong.
>
> Since we performed a lot of slab geometry simulatin and gmx worked 
> perfect in version 3.3 and 4.5, when we use 4.6 and higher, we find 
> this problem. Is this a bug or my setup error in mdp？
>
> --
> PhD student
> State Key Laboratory of Coal Combustion,
> School of Energy and Power Engineering,
> Huazhong University of Science and Technology (HUST),
> Room 302 Power Building,
> 1037 Luoyu Road, Wuhan, Hubei 430074 China
> Email: chrishengbee at hust.edu.cn
> Phone: (86)27-87548122
> http://itp.energy.hust.edu.cn
>
>
>

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