[gmx-users] Liquid-liquid interface and electric field
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 16 17:02:24 CET 2016
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
> 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,
> 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
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