)))) If I find resources for several calculations (the last one continued for 20 days) I'll try both methods and will share You. It seems I should find another smaller test system and reproduce the approaches. Thank You
Sun May 20 09:55:14 CEST 2018 ------------------------------ I think CompEl is described in the manual, the options for it are here: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html I've never used it, so I can't suggest anything, but you can ask on this board for specific mdp examples. The way CompEl works is conceptually simple: it maintains a transmembrane ionic concentration gradient by swapping ions across the periodic boundary. The result is that on average you get a voltage of (kT/q)log(c_above/c_below) across the system. In reality, you get noisy results (see Fig. 3 (b) in http://www.mpibpc.mpg.de/grubmueller/compel ). On the other hand, if you have long simulated times, you can still get clean data. The problem with using a constant field is that it is only physical for a system with a nearly constant dielectric throughout. I am guessing that is not your case and you have water (epsilon ~80) and a lipid membrane (eps ~ 5?). If there was a real voltage across such a box, it would almost entirely drop across the membrane (i.e. high field across membrane and low field elsewhere). This is why I prefer to use fields that are as low as computationally possible. I would try CompEl at least out of curiosity. In principle, it is a solid idea, but I think this algorithm is clunky and how it agrees with PBC is unclear to me. If you get clean and reasonable data, please let everyone know! :) Alex On 5/20/2018 1:16 AM, alex rayevsky wrote: >* Dear Alex! *>>* Yes, I thought about all Your reflections and I'm also not sure that CompEl *>* is well parameterzied for a non-specialist like me and the electric field *>* is more intuitive for me. However, when I saw the dimension 'V/nm' for the *>* first time, I thought that something must depend on the length of the axis *>* of application (in my case it is about 12 nm) or the thickness of the *>* membrane. *>* These two of 20 articles I've found on the theme befor wrote in gmx *>* society: *>* Structural and Functional Effect of an Oscillating Electric Field on the *>* Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study. ( DOI: *>* 10.1371/journal.pone.0166412 ) and Molecular dynamics of ion transport *>* through the open conformation of a bacterial voltage-gated sodium channel. *>* ( https://doi.org/10.1073/pnas.1214667110 <https://doi.org/10.1073/pnas.1214667110>). ANd this method works fine, in *>* general, they've got what they wanted. *>* But there is no full description of parameterization. what can You say? *>>* Thank You *>>>* At the same time compel method is very popular too, here is another mention *>* of CompEl - http://dx.doi.org/10.1016/j.bpj.2017.02.016 <http://dx.doi.org/10.1016/j.bpj.2017.02.016> *>>>* Alex <https://www.mail-archive.com/[email protected]&q=from:%22Alex%22 <https://www.mail-archive.com/[email protected]&q=from:%22Alex%22>> *>* Sat, 19 May 2018 17:35:15 -0700 *>* <https://www.mail-archive.com/[email protected]&q=date:20180519 <https://www.mail-archive.com/[email protected]&q=date:20180519>> *>>* It's more of a philosophical question in, unfortunately. I don't use *>* CompEl, because I believe it is conceptually clunky, but that's a *>* matter of opinion that could turn into discussion beyond the scope of *>* your question. I don't study biomolecules, so I can get away with *>* applying direct fields. For biomolecules, however, I do suggest at *>* least looking into CompEl and how it works, and then choosing *>* appropriate setup sothat you do not slow down your simulation too *>* much. *>>* That said, 0.4 V/nm does not really correspond to 40 mV in any way. The best *>* "fake" guess is that the voltage drop across the entire box is its height, *>* times the value of E-z. It is fake, because your field has nothing to do *>* with the solution of the Poisson's equation, or the box height. The *>* consequences of this field do, but the field itself doesn't, if that makes *>* sense. One other point to be made: water's dielectric breakdown threshold *>* is around 100 MV/m = 0.1 V/nm. Noone in the community that publishes in *>* Biophysical Journal seems to care about it, but huge simulated fields can *>* be incompatible with what's being studied. *>>* My response probably doesn't help much, but this is the situation with all *>* MD software that relies on Ewald summation. *>>* Alex *>>>* On 5/19/2018 5:16 PM, alex rayevsky wrote: *>>* Dear all, *>>* Which protocol, Electric field section or the CompEl, I should use in the *>* situtation: *>* 1. I built an ion channel by homology, prepared a bilayer membrane, embeded *>* my protein and run a simulation to relax the system (100 ns) *>* 2. my channel was closed all the time. *>* 3. I want to run four parallel simmulations, starting from the relaxed *>* state: *>* a) system under the effect of -80 mV and under +40 mV - the second one *>* should cause a pore opening; *>* b) both previous variants with a ligand in the pore; *>>* The voltage sensitive domain of the Nav channel should respond to the *>* electric stimuli, that is why I thought it is reasonable to apply it to Z *>* direction and assign electric-field-z = 0.4 0 0 0 for +40mV state, for *>* example. other parameters should stay intact, I think, because I don't know *>* if they should be changed... *>>* at the same time I've read several different works when CompEl was *>* implemented to the membrane-channel systems. The end of the *>* pagehttp://www.mpibpc.mpg.de/grubmueller/compel duplicates a gromacs *>* manual, *>* however I didn't find any mention of a voltage handling and what exactly *>* I'll obtain at the end.... *>* Which method is more approrpiate for my task? *>>* Thank You !! *>>>>>>* *Nemo me impune lacessit* * *Nemo me impune lacessit* -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
