Dear gmx users, I'm trying to simulate change in the ion flux upon mutations using Computational electrophysiology (compEL). I have used packmol-memgen in order to generate the double bilayer using a salt concentration of 1 M (3216 Cl- and 3168 K+). Then, I have setted up the simulation following the compEL protocol. However, after 50 ns of simulation, I still have two big issues:
1) In the swapions logfile I've got a huge number of warnings regarding ions that moved from Domain_B to Domain_A probably throught the membrane (checking the movie with VMD it seems they move across the boundaries). I thought to tackle this issue by increasing the water layer. 2) In the same way, watching the movie I have notice that ions enter the channel (the pore radius is about 3 A) but they do not cross from one domain to the other. I think I may have misunderstood the protocol, because in numerous article they talk about setting an ionic imbalance between compartments. However, I have not performed it in any step. Do I have to manually set an ionic imbalance (and, in this case there are a tool to perform it?) or it should be set by the input compEL file? I have used the following inputs: ; Ion/water position swapping for computational electrophysiology setups ; Swap positions along direction: no, X, Y, Z swapcoords = Z adress = no ; Swap attempt frequency. This determines how often a swap attempt will be made. Since therefore the positions of the ions, solvent, and swap groups are communicated around, this is a time-consuming opera tion. Do not try to swap every step, this will slow down the simulation a lot. swap-frequency = 100 ; Two index groups that contain the compartment-partitioning atoms split-group0 = channel1 split-group1 = channel2 ; Use center of mass of split groups (yes/no), otherwise geometrical center is used. Choose two index groups that divide the MD system into two compartments, here in Z-direction. If massw-split is activat ed, this group's center of mass will be used as the dividing point, if not, the geometrical center is used. If you choose a membrane channel as split group, then the center of the channel will define the compartment-dividing plane. massw-split0 = no massw-split1 = no ; Group name of solvent molecules solvent-group = Water ; Average the number of ions per compartment over these many swap attempt steps. If coupl-steps is set to 1, then the instantaneous ion distribution will determine whether ions are exchanged. coupl-steps > 1 will use the time-averaged ion distribution instead. This is useful when > ions are diffusing around near compartment boundaries (in the channel for > example) which would lead to numerous in- and outswap s for coupl-steps=1. coupl-steps = 10 ; Number of ion types to be controlled iontypes = 2 ; Names of the ion types that can be exchanged with solvent molecules ; -1 means fix the numbers as found in time step 0. These numbers have to add up to the total number of ions present in the swap group. iontype0-name = Cl-_Cl- iontype0-in-A = -1 ; requested number of Cl ions in compartment A iontype0-in-B = -1 ; requested number of Cl ions in compartment B iontype1-name = K+_K+ iontype1-in-A = -1 ; requested number of K+ ions in compartment A iontype1-in-B = -1 ; requested number of K+ ions in compartment B ; Offset compartment-defining layers bulk-offsetA = 0.0 bulk-offsetB = 0.0 ; Split cylinder: radius, upper and lower extension (nm) (for counting on-the-fly diagnostics, has no influence on whether or not ions are swapped) cyl0-r = 0.7 cyl0-up = 3 cyl0-down = 3 cyl1-r = 0.7 cyl1-up = 3 cyl1-down = 3 ; Start to swap ions if threshold difference to requested count is reached. A threshold of 1 means that a swap is performed if the average ion count in a compartment differs by 1 ore more from the request ed values. Higher thresholds mean that larger differences are accepted. Ions are also only swapped until the requested number +/- the threshold is reached. threshold = 1 ; User defined thingies user1-grps = user2-grps = userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 ; Electric fields ; Format for electric-field-x, etc. is: four real variables: ; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps), ; and sigma (ps) width of the pulse. Omega = 0 means static field, ; sigma = 0 means no pulse, leaving the field to be a cosine function. electric-field-x = 0 0 0 0 electric-field-y = 0 0 0 0 electric-field-z = 0 0 0 0 Thank you very much for your help and I'm sorry if some questions sound silly, but I am a novel gmx user. Regards. -- 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 gmx-users-requ...@gromacs.org.
