[gmx-users] Liquid-liquid interface and electric field

Gschwend Grégoire gregoire.gschwend at epfl.ch
Mon Nov 21 08:08:13 CET 2016 

I have tried to change the input as you suggested and it worked, I can see the ions transfer through the interface. 

Thank you for your help!
________________________________________
De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> de la part de David van der Spoel <spoel at xray.bmc.uu.se>
Envoyé : vendredi 18 novembre 2016 07:13
À : gmx-users at gromacs.org
Objet : Re: [gmx-users] Liquid-liquid interface and electric field

On 17/11/16 19:37, Gschwend Grégoire wrote:
> So, I have run gmx dump on the tpr file that I produce with grompp (using exactly the parameters given below) and it actually looks like no field is applied. Indeed, gmx dump give the following lines:
>
>    E-x:
>       n = 0
>    E-xt:
>       n = 0
>    E-y:
>       n = 0
>    E-yt:
>       n = 0
>    E-z:
>       n = 0
>    E-zt:
>       n = 0
>
> Am I doing something wrong with the syntax of the input?

If this is the input (from your previous mail)

E-1;E-1;E-0

then yes. It should be

; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x                      =
; Time dependent (pulsed) electric field. Format is omega, time for pulse
; peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving
; the field to be a cosine function.
E-xt                     =


> ________________________________________
> De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> de la part de David van der Spoel <spoel at xray.bmc.uu.se>
> Envoyé : jeudi 17 novembre 2016 16:10
> À : gmx-users at gromacs.org
> Objet : Re: [gmx-users] Liquid-liquid interface and electric field
>
> On 16/11/16 20:36, Gschwend Grégoire wrote:
>> Tank you for the comment on the parameters. The system is neutral.
>>
>> I do no think that the problem is the energy barrier because in that case the ions would be blocked at the interface but they would at least move in the direction imposed by the field (and not randomly move in their respective phases). Do you know if their is a way to check that the field is really applied?
>
> You can pass the option -field to mdrun to print the applied field. You
> can also run gmx dump -s topol.tpr | less
> I would expect the ions to diffuse normally (randomly) just a little bit
> more in the direction of the field.
> You may also try analysis tools, maybe gmx current
>
>
>> ________________________________________
>> De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> de la part de David van der Spoel <spoel at xray.bmc.uu.se>
>> Envoyé : mercredi 16 novembre 2016 17:02
>> À : gmx-users at gromacs.org
>> Objet : Re: [gmx-users] Liquid-liquid interface and electric field
>>
>> On 16/11/16 11:54, Gschwend Grégoire wrote:
>>> Thank you for yor answer.
>>>
>>> So, with and without electric field the ions move, sometimes form pairs or separate, etc. Everything looks "normal". The temperature of the box is stable at 300K, and the pressure around 1bar. The size of the box is stable as well. The simulation lasts 2 ns. I think that this simulation time should be enough to see an ion transfer. For instance, the simulation length was 200 ps with a field of 0.5 V/nm in this publication:  J. Phys. Chem. A., 103, 10274-10279 (1999),  (http://pubs.acs.org/doi/abs/10.1021/jp991967w).
>>>
>>> Please find below the parameters that I use for the simulation, maybe this could help...
>>>
>> For your parameters, please consider setting
>> fourierspacing = 0.12
>> and use just one group for t coupling. I hope your simulation system is
>> neutral in order to prevent artifacts.
>>
>> It could be that the energy barrier is too high which you could find out
>> using a PMF calculation.
>>
>>> constraint_algorithm    = lincs
>>> constraints               = all-bonds
>>> lincs_iter                = 1
>>> lincs_order               = 4
>>>
>>> integrator    = md
>>> nsteps                = 2000000
>>> dt                = 0.001
>>>
>>> cutoff-scheme   = Verlet
>>> ns_type                   = grid
>>> nstlist                   = 10
>>> rcoulomb          = 1.0
>>> rvdw              = 1.0
>>> coulombtype       = PME
>>> pme_order         = 4
>>> fourierspacing        = 0.16
>>>
>>> tcoupl                = V-rescale
>>> tc-grps               = Aqueous Organic
>>> tau_t         = 0.5 0.5
>>> ref_t         = 300 300
>>> pcoupl                        = Berendsen
>>> pcoupltype            = semiisotropic
>>> tau_p                 = 5.0
>>> ref_p                 = 1.0 1.0
>>> compressibility     = 4.5e-5 4.5e-5
>>>
>>> E-1;E-1;E-0
>>>
>>> refcoord_scaling    = com
>>> pbc           = xyz
>>> DispCorr      = EnerPres
>>> gen_vel               = no
>>>
>>> ________________________________________
>>> De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> de la part de David van der Spoel <spoel at xray.bmc.uu.se>
>>> Envoyé : mercredi 16 novembre 2016 11:09
>>> À : gmx-users at gromacs.org
>>> Objet : Re: [gmx-users] Liquid-liquid interface and electric field
>>>
>>> On 16/11/16 09:51, Gschwend Grégoire wrote:
>>>> Hello everyone,
>>>>
>>>>
>>>> I am trying to simulate an ion transfer at an interface between two immiscible electrolytes solutions. I have prepared a 5x5x5 nm box with the solvents and electrolytes. The system is stable and well equilibrated. The problem now is that when I apply an electric field in the z direction (normal to the interface)  it seems that nothing happens. By nothing I mean nothing different that with a simulation without electric field. I have tried many values for the magnitude of the field, even unrealistic values as high as 5 V/nm (while the ions should transfer around 0.5 V/nm max).
>>>>
>>>>
>>>> In the simulation I use periodic boudary conditions in all three directions. Thus, I was wondering if this was compatible with an electric field in the z direction. Indeed, the PBC implies that the potential is the same at z=0 and z=box_size, which implies that there is no field. Of couse the field could be periodic, but in the manual it is said that the frequency of the cosine is zero.
>>>>
>>>>
>>>> Should I use walls and PBC in x and y directions only?
>>> No, that should not be necessary.
>>> Please be more specific than "nothing happens". Does the ion not move at
>>> all? Then the temperature is zero. How long is the simulation?
>>>>
>>>>
>>>> Thank you for your help and suggestions,
>>>>
>>>>
>>>> Grégoire
>>>>
>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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