Thank you very much. In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?)
Regards, -Aswathy On Thu, Jun 17, 2010 at 7:52 PM, <[email protected]> wrote: > Determining how many waters is sufficient is a tough problem, try > successive runs of option #3, below. As for the simpler topic of getting > more hydration: > > 1. If the issue is simply getting the channel hydrated enough to overcome > some transition from dry to wet, then run a neat water box od 216 spc for > 100 ps and extract a frame every 10 ps, then run genbox 10x successively > using each of these frames. This should give you massive hydration. > > 2. If that doesn't work, then you could add a new equilibration step where > you posres some cap waters so that the channel can not dry out. This may > allow SC's to equilibrate to a wet environment. > > 3. If the issue is that the water is still moving out, then why not do SMD > on a water into the pore and find out where the repulsion is. > > -- original message -- > > Hi everyone, > > I have a homology model of a transporter. I want to study the ligand > transport through the channel. i have done the following steps. > > 1. Ligand has docked to the mouth of the channel > 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated > for 4ns(with position restarint on Protein & ligand) > 3. Then I saw tht there are very few wtaer inside the pore, Since this > channel is an aqueous pore, I have added water to the channel using genbox. > 4. Then the complete system equilibrated for pico seconds. > 5,in order to select different snap shots for SMD (want to do a multiple > SMDs with different starting structures.) I have run 1ns Production run and > selected different frames. > > Suddenly I found that still there is no enough water in the pore, the water > is moving away from the channel during step 4 &5? > > How can I solve this problem? Also how will I know how many water molecules > will be sufficient for the channel? > > Thanks for your support. > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy
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