[gmx-developers] Question about ewald_LRcorrection() function

[Berk Hess]

Hi,

I think you misinterpreted the code in ewald_LRcorrection. It does the 
same things in 3.3.1 and 4.6.7.
My guess is that the issue you are observing is due to periodic boundary 
conditions. With group cut-off scheme charge groups are whole (not split 
by PBC), so water molecules are usually whole. Then the 3DC correction 
always works correctly when you have charge groups with zero net charge. 
In the Verlet cut-off scheme with domain decomposition, or with charged 
charge groups, (partial) charges moving over PBC change the system 
dipole. To get your system to run correctly you need to ensure that no 
water molecule moves over the periodic boundary in along the 
z-dimension. I think grompp will print a warning for this issue.

Cheers,

Berk

On 2016-06-07 10:12, Sheng Bi wrote:
>
> Sorry, some type-offs in previous question.
>
> In gmx-4.6.7, ewald_LRcorrection()*.* We loop over excluded neighbours 
> only in condition *calc_excl_corr=1*. But when using Verlet cut-off 
> scheme, *calc_excl_corr will be 0*.
>
> --
> 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
>
> *From: *Sheng Bi <mailto:chrishengbee at hust.edu.cn>
> *Sent: *Tuesday, June 7, 2016 1:28 AM
> *To: *gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>
> *Subject: *[gmx-developers] Question about ewald_LRcorrection() function
>
> Dear GMX developers:
>
>                I find a abnormal phenomenon when using 
> *gromacs-4.6.7*. I set up a system containing two walls(consist of 
> freeze atoms), one wall has positively charges on atoms, another has 
> negatively charges.  I put an water molecule(rigid spc/spce/tip3p 
> model) between these two walls. *Whole system seems like below*:
>
> ****************************************
>
>                * - H +                                          *
>
>                * -             \                + 
> vacuum                              *
>
>               * -   O +                                          *
>
>                * -  / +                                          *
>
>                * -          H                
> +                                          *
>
> ****************************************
>
>                I use *Verlet cut-off scheme, PME method, and 
> ewald-geometry=3DC*. Temperature of whole system is at *0K*, 
> controlled by *v-rescale method*. I run whole simulation *only in 
> OPENMP parallel*.
>
>                One can have following expected behavior of water 
> molecule without MD simulation: Since it can be seen as an infinite 
> panel capacitor, *there is constant electric field between two walls. 
> So the water will change it orientation, but won’t change it’s 
> position(Since 0K)*.
>
>                This phenomenon can be *confirmed by gromcas-3.3.1* 
> (although there is position shift, but quite small). Also, if one use 
> higher version of gromacs, such as 4.6.7 or higher *with 
> ewald-geometry=3D, either no problem*. However, if one use *3DC* (and 
> it should be), you can see *an obvious force on water molecule*.
>
>                I hacked into source code, and find this might due to 
> *ewald_LRcorrection()* function:
>
>                Firstly, in gmx-4.6.7, ewald_LRcorrection()*.* We *loop 
> over excluded neighbours only in condition calc_excl_corr=0. But when 
> using verlet cut-off scheme, calc_excl_corr will be 1*. In gmx-3.3.1, 
> we do loop over excluded neighbours without additional if() statement.
>
>                Secondly, in gmx-4.6.7, , ewald_LRcorrection(). When do 
> dipole correction on force, we loop over *excl_load* (Exclusion load 
> distribution over the threads). In fact, most water model will have 
> nrexel=2. So, as a result, we *only do dipole correction on O atom, 
> but do nothing on H atoms* and we will see an obvious force on the 
> whole water molecule. I think this is not purpose of 3DC。
>
>                Best regards！
>
> Sheng Bi
>
> **
>
> ---
> 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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