[gmx-developers] Question about ewald_LRcorrection() function
Sheng Bi
chrishengbee at hust.edu.cn
Tue Jun 7 17:05:02 CEST 2016
Hi Berk,
Thanks for your response!
However, my question is still there. In fact, I run simulation in one core (with multi-threadings), so domain decomposition could not be the reason for this phenomenon. Meanwhile, we use a quite large box (due to 3DC, Z length usually need a huge vacuum), so I think the water is within the box.
Actually, I have printed dipcorrA for both gmx331 and gmx467 and find that there is no difference. So it wouldn’t be the PBC trouble.
I think you are right about ewald_LRcorrection(). I check this function further and think it works fine.
However, I think there is something wrong in forcerec_set_excl_load() function (in forcerec.c file). We know in ewald_LRcorrection(), for each thread, we loop over (i = fr->excl_load[t]; i < fr->excl_load[t+1]) to do dipole correction. The excl_load array is calculated in forcerec_set_excl_load(), as shown in following:
/ ****** line 3018 ********* /
for (t = 1; t <= fr->nthreads; t++)
{
ntarget = (ntot*t)/fr->nthreads;
while (i < top->excls.nr && n < ntarget)
{
for (j = ind[i]; j < ind[i+1]; j++)
{
if (a[j] > i)
{
n++;
}
}
i++;
}
fr->excl_load[t] = i;
}
Suppose we have a system consisted by 2 types of molecules. The whole system contains 2 atoms, 1 for molecule A(positively charged) and 1 for molecule B(negatively charged). We perform simulation in one core with one thread. So, for code above, we can deduce parameters like following:
top->excls.nr = 2
fr->nthreads = 1
ntarget = ntot =1
Since it use while() statement here, we can deduce that:
fr->excl_load[0] =0
fr->excl_load[1] =1
However, fr->excl_load[1] should be 2. This wrong value lead to missing a dipole correction on the 2th atom in ewald_LRcorrection(). Because in ewald_LRcorrection(), we loop from fr->excl_load[0]=0 to fr->excl_load[1] =1 using for statement.
I think this is the direct reason for wrong additional force on water molecule in my system. This error might result big trouble when someone using umbrella sampling in a system with system dipole.
Please correct me if I am wrong.
Best regards!
Sheng
--
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: Berk Hess
Sent: Tuesday, June 7, 2016 5:49 PM
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] Question about ewald_LRcorrection() function
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
Sent: Tuesday, June 7, 2016 1:28 AM
To: 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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